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#51
General / Re: about the Torsion in molec...
Last post by raspa666 - June 12, 2023, 12:35:05 PMWow! Thank you very much, Mateusz!
It is really helpful !!! :) :) :)
I know how to deal with the data now. :)
It is really helpful !!! :) :) :)
I know how to deal with the data now. :)
#52
General / Re: about the Torsion in molec...
Last post by plgmattpokora - June 12, 2023, 11:55:08 AMHi,
you have to look for the units in the RASPA2 manual. For example:
HARMONIC_BOND
describes bonds and needs two parameters with units K/A^2, A.
From the LigParGen server, you can get the topologies in different formats. I used the GROMACS itp file, the units used in GROMACS can be found here: https://manual.gromacs.org/current/reference-manual/topologies/topology-file-formats.html
So GROMACS uses units kJ/(mol*nm^2), nm. The conversion from nm to A is straightforward, but in the first case we need:
a) convert from kJ/mol to J (multiply by 1000 and divide by Avogadro's constant),
b) convert from nm^-2 to A^-2 (divide by 100),
c) convert from J/A^2 to K/A^2 (divide by Boltzmann's constant)
that brings us to multiply the value from GROMACS' itp file by 1.2037. In the same manner, you would obtain SIX_COSINE_DIHEDRAL potential in RASPA2 from GROMACS' RB dihedral parameters values by multiplying them by 120.272355. Please refer to the manual of RASPA2. And also please be aware that if you have no experience with such simulations, it can take a few days (or even weeks) to understand how to prepare inputs properly and run the simulations correctly.
Also, as you will be preparing the forcefield description, please pay attention to the Lennard-Jones parameters. You need to perform such a conversion as well. In some cases, like in the case of the Dreiding forcefield, you also need to check if the values are scaled in relation to the equation used in RASPA2. You need to read the manual and papers to understand everything correctly, and that can be challenging.
Cheers,
Mateusz
you have to look for the units in the RASPA2 manual. For example:
HARMONIC_BOND
describes bonds and needs two parameters with units K/A^2, A.
From the LigParGen server, you can get the topologies in different formats. I used the GROMACS itp file, the units used in GROMACS can be found here: https://manual.gromacs.org/current/reference-manual/topologies/topology-file-formats.html
So GROMACS uses units kJ/(mol*nm^2), nm. The conversion from nm to A is straightforward, but in the first case we need:
a) convert from kJ/mol to J (multiply by 1000 and divide by Avogadro's constant),
b) convert from nm^-2 to A^-2 (divide by 100),
c) convert from J/A^2 to K/A^2 (divide by Boltzmann's constant)
that brings us to multiply the value from GROMACS' itp file by 1.2037. In the same manner, you would obtain SIX_COSINE_DIHEDRAL potential in RASPA2 from GROMACS' RB dihedral parameters values by multiplying them by 120.272355. Please refer to the manual of RASPA2. And also please be aware that if you have no experience with such simulations, it can take a few days (or even weeks) to understand how to prepare inputs properly and run the simulations correctly.
Also, as you will be preparing the forcefield description, please pay attention to the Lennard-Jones parameters. You need to perform such a conversion as well. In some cases, like in the case of the Dreiding forcefield, you also need to check if the values are scaled in relation to the equation used in RASPA2. You need to read the manual and papers to understand everything correctly, and that can be challenging.
Cheers,
Mateusz
#53
General / Re: about the Torsion in molec...
Last post by raspa666 - June 12, 2023, 10:13:40 AMThank U, Mateusz！ :)
I am interesting in a moluecule --- CH3COOH, however, i can not find a mol.def file in the raspa-molecules. So I try to write a def file.
emmm, you mentioned that 'use the proper units of the parameters ', but if I try the OPLS-AA forcefield, how can I tranfersform the parameters/unit to a right one?
I have no idea...
Hoping you response.
Thank U ! :)
I am interesting in a moluecule --- CH3COOH, however, i can not find a mol.def file in the raspa-molecules. So I try to write a def file.
emmm, you mentioned that 'use the proper units of the parameters ', but if I try the OPLS-AA forcefield, how can I tranfersform the parameters/unit to a right one?
I have no idea...
Hoping you response.
Thank U ! :)
#54
General / Re: about the Torsion in molec...
Last post by plgmattpokora - June 12, 2023, 09:36:32 AMHi,
the parameters that describe the torsion angles (as well as other parameters describing both the bonding and non-bonding interactions) are a part of a specific forcefield, in the example you provided, the TraPPE forcefield. You did not specify what molecule you are interested in. You can find the TraPPE forcefield description here: http://trappe.oit.umn.edu/. You can find there, for example, 2,3-dimethylbutane, which shares the dihedral parameters with 2-methylbutane.
Bear in mind, however, that description of a molecule within a forcefield is not an easy task. You can also try the OPLS-AA forcefield in a case you cannot find your molecule within the TraPPE, here is a generator of the parameters: http://zarbi.chem.yale.edu/ligpargen/
In either case please remember to make sure you use the proper units of the parameters in RASPA. It may be also a good thing if you read a bit about the forcefields in atomistic simulations.
Cheers,
Mateusz
the parameters that describe the torsion angles (as well as other parameters describing both the bonding and non-bonding interactions) are a part of a specific forcefield, in the example you provided, the TraPPE forcefield. You did not specify what molecule you are interested in. You can find the TraPPE forcefield description here: http://trappe.oit.umn.edu/. You can find there, for example, 2,3-dimethylbutane, which shares the dihedral parameters with 2-methylbutane.
Bear in mind, however, that description of a molecule within a forcefield is not an easy task. You can also try the OPLS-AA forcefield in a case you cannot find your molecule within the TraPPE, here is a generator of the parameters: http://zarbi.chem.yale.edu/ligpargen/
In either case please remember to make sure you use the proper units of the parameters in RASPA. It may be also a good thing if you read a bit about the forcefields in atomistic simulations.
Cheers,
Mateusz
#55
General / about the Torsion in molecule....
Last post by raspa666 - June 12, 2023, 09:14:10 AMFor example, in the 2-methylbutane.def, there is a section of '# Torsion n1-n2-n3-n4 type'
# Torsion n1-n2-n3-n4 type
0 1 2 3 TRAPPE_DIHEDRAL -251.06 428.73 -111.85 441.27
4 1 2 3 TRAPPE_DIHEDRAL -251.06 428.73 -111.85 441.27
How can we get the 4 value of TRAPPE_DIHEDRAL(-251.06 428.73 -111.85 441.27)?
Is there a software that can output a data file containing this value?
Thank U! :)
# Torsion n1-n2-n3-n4 type
0 1 2 3 TRAPPE_DIHEDRAL -251.06 428.73 -111.85 441.27
4 1 2 3 TRAPPE_DIHEDRAL -251.06 428.73 -111.85 441.27
How can we get the 4 value of TRAPPE_DIHEDRAL(-251.06 428.73 -111.85 441.27)?
Is there a software that can output a data file containing this value?
Thank U! :)
#56
Bug reports / Re: Segmentation fault related...
Last post by Z.GAO - June 08, 2023, 12:35:23 PMI had the same problem. I wonder if you have solved this problem?
#57
General / Warning messages during enthal...
Last post by sridhar - June 02, 2023, 12:29:20 PMHi,
I am getting the following warning while calculating the enthalpy of the adsorption in ZIF-8.
WARNING: THE SYSTEM HAS A NET CHARGE
WARNING: THERE ARE ATOM-PAIRS WITH NO VDW INTERACTION Zn1-H2 Zn1-N1 Zn1-H3A Zn1-H3B Zn1-H3C C1-H2 C1-N1 C1-H3A C1-H3B C1-H3C C2-H2 C2-N1 C2-H3A C2-H3B C2-H3C C3-H2 C3-N1 C3-H3A C3-H3B C3-H3C C_co2-H2 C_co2-N1 C_co2-H3A C_co2-H3B C_co2-H3C O_co2-H2 O_co2-N1 O_co2-H3A O_co2-H3B O_co2-H3C H2-Zn1 H2-C1 H2-C2 H2-C3 H2-C_co2 H2-O_co2 H2-N1 H2-H3A H2-H3B H2-H3C N1-Zn1 N1-C1 N1-C2 N1-C3 N1-C_co2 N1-O_co2 N1-H2 N1-H3A N1-H3B N1-H3C (maximum 50 interactions shown)
The simulation.input file is attached. What could be the reason behind the warning, and would it affect the final solution ?
Thank you.
Regards
Sridhar
I am getting the following warning while calculating the enthalpy of the adsorption in ZIF-8.
WARNING: THE SYSTEM HAS A NET CHARGE
WARNING: THERE ARE ATOM-PAIRS WITH NO VDW INTERACTION Zn1-H2 Zn1-N1 Zn1-H3A Zn1-H3B Zn1-H3C C1-H2 C1-N1 C1-H3A C1-H3B C1-H3C C2-H2 C2-N1 C2-H3A C2-H3B C2-H3C C3-H2 C3-N1 C3-H3A C3-H3B C3-H3C C_co2-H2 C_co2-N1 C_co2-H3A C_co2-H3B C_co2-H3C O_co2-H2 O_co2-N1 O_co2-H3A O_co2-H3B O_co2-H3C H2-Zn1 H2-C1 H2-C2 H2-C3 H2-C_co2 H2-O_co2 H2-N1 H2-H3A H2-H3B H2-H3C N1-Zn1 N1-C1 N1-C2 N1-C3 N1-C_co2 N1-O_co2 N1-H2 N1-H3A N1-H3B N1-H3C (maximum 50 interactions shown)
The simulation.input file is attached. What could be the reason behind the warning, and would it affect the final solution ?
Thank you.
Regards
Sridhar
#58
General / Re: Very beginner question
Last post by plgmattpokora - May 23, 2023, 03:10:57 PMHi,
my experience with RASPA is not great, but it took me a few weeks to set my system up properly, so I can share with you some advice:
1) in the force_field_mixing_rules.def file you put the non-bonding interactions, which in your case probably means the Lennard-Jones epsilon and sigma values (yes, epsilon/kb as given the SI). Pay attention to the cut-off defined in the simulation.input as well as if there are tail corrections applied to the potential. In force_field.def you explicitly define interactions (meaning you'd have to define C-C, C-O, C-H, etc.). In most cases anyway, the forcefields utilize the mixing rules, so you do not have to do that. In that case, you leave the force_field.def "empty" (not literally empty, there is still some input that says there are no rules to overwrite. Just look at the example forcefields provided with RASPA).
2) in the pseudo_atoms.def file you define (in most cases) the atoms of your adsorbate. That means you define what atoms create your molecule by assigning appropriate chemical elements and masses to the atoms (as you can see in the provided files). The labels used in that file must correspond to the ones used in the molecule.def file later. As you want to study CO2/H2O adsorption, and the paper you linked is about alkanes, you have to find the parameters (both for LJ and charges) somewhere else. It can be TraPPE in the case of CO2, and you have plenty of water models to choose from. The charges should be provided there.
3) charges of the MOFs in the SI: the best option is to include them directly in the CIF file. Look at the CIFs distributed with RASPA, you just define a new field in the CIF and that's it. Of course, make sure you match atoms between your CIF file and the ones in the SI. Your CIF may have more atoms than in the SI: either your CIF does not describe the smallest asymmetric unit or/and your CIF describes different symmetry, hence the difference in the number of atoms. If you have used VASP for the geometry optimization, you can probably get the DDEC charges as well if there is a mismatch between their description of the MOF and yours. You can also use built-in charge equilibration method to get the charges, or use some machine learning-based charges (google for PACMOF, for example).
Again, I may be wrong as I still learn RASPA and MC in general. You will also have to spend a lot of hours learning how to use RASPA.
Cheers,
Mateusz
my experience with RASPA is not great, but it took me a few weeks to set my system up properly, so I can share with you some advice:
1) in the force_field_mixing_rules.def file you put the non-bonding interactions, which in your case probably means the Lennard-Jones epsilon and sigma values (yes, epsilon/kb as given the SI). Pay attention to the cut-off defined in the simulation.input as well as if there are tail corrections applied to the potential. In force_field.def you explicitly define interactions (meaning you'd have to define C-C, C-O, C-H, etc.). In most cases anyway, the forcefields utilize the mixing rules, so you do not have to do that. In that case, you leave the force_field.def "empty" (not literally empty, there is still some input that says there are no rules to overwrite. Just look at the example forcefields provided with RASPA).
2) in the pseudo_atoms.def file you define (in most cases) the atoms of your adsorbate. That means you define what atoms create your molecule by assigning appropriate chemical elements and masses to the atoms (as you can see in the provided files). The labels used in that file must correspond to the ones used in the molecule.def file later. As you want to study CO2/H2O adsorption, and the paper you linked is about alkanes, you have to find the parameters (both for LJ and charges) somewhere else. It can be TraPPE in the case of CO2, and you have plenty of water models to choose from. The charges should be provided there.
3) charges of the MOFs in the SI: the best option is to include them directly in the CIF file. Look at the CIFs distributed with RASPA, you just define a new field in the CIF and that's it. Of course, make sure you match atoms between your CIF file and the ones in the SI. Your CIF may have more atoms than in the SI: either your CIF does not describe the smallest asymmetric unit or/and your CIF describes different symmetry, hence the difference in the number of atoms. If you have used VASP for the geometry optimization, you can probably get the DDEC charges as well if there is a mismatch between their description of the MOF and yours. You can also use built-in charge equilibration method to get the charges, or use some machine learning-based charges (google for PACMOF, for example).
Again, I may be wrong as I still learn RASPA and MC in general. You will also have to spend a lot of hours learning how to use RASPA.
Cheers,
Mateusz
#59
General / Very beginner question
Last post by extremesonic01 - May 22, 2023, 07:29:07 PMHello
I never tried MC or RASPA before, and now I'm trying to learn raspa. I just tried some examples and tutorial during last few weeks, and I'm trying to set up my own MC simulation using RASPA adsorption of Co2 and H2O on some MOF structure for adsorption isotherm.
I prepared some input cif files from vasp. Then look for force field, found one publication:
https://pubs.rsc.org/en/content/articlelanding/2018/CP/C8CP05750H
Authors kindly provided force field parameters in supplementary files:
https://www.rsc.org/suppdata/c8/cp/c8cp05750h/c8cp05750h1.pdf
Now, I need to prepare pseudo atom, force field mixing rules, and force field files. But I'm not sure how should I use these parameters of supplementary files of the paper to input force field files. Should I need to write e/kb and sigma values to force field mixing rules? Or force field?
For pseudo atom file, I write down almost all data per each atoms from googling except charge. I'm not sure how could I determine the charge value for pseudo atom. Is this should be "partrial charge" values provided by supplementary file?
Thanks!
I never tried MC or RASPA before, and now I'm trying to learn raspa. I just tried some examples and tutorial during last few weeks, and I'm trying to set up my own MC simulation using RASPA adsorption of Co2 and H2O on some MOF structure for adsorption isotherm.
I prepared some input cif files from vasp. Then look for force field, found one publication:
https://pubs.rsc.org/en/content/articlelanding/2018/CP/C8CP05750H
Authors kindly provided force field parameters in supplementary files:
https://www.rsc.org/suppdata/c8/cp/c8cp05750h/c8cp05750h1.pdf
Now, I need to prepare pseudo atom, force field mixing rules, and force field files. But I'm not sure how should I use these parameters of supplementary files of the paper to input force field files. Should I need to write e/kb and sigma values to force field mixing rules? Or force field?
For pseudo atom file, I write down almost all data per each atoms from googling except charge. I'm not sure how could I determine the charge value for pseudo atom. Is this should be "partrial charge" values provided by supplementary file?
Thanks!
#60
Input files and parameters / Generating framework.def and l...
Last post by shu815 - May 17, 2023, 09:28:39 PMHello!
I have a question about utilizing flexible frameworks in a GCMC simulation in Raspa:
Is there an easy way to generate a cif which is labeled by atom types such that each atom type can be uniquely defined in bonds/angles/dihedrals/impropers a framework.def file? I hope to write my own framework.def file for UFF atom types, I see that there are some example framework.def files in the examples directory in the RASPA install, but they don't seem to have all the types in UFF e.g. C atoms in rings C_R.
One approach I was thinking of using was taking a cif -> lammps datafile generated from the lammps_interface from Boyd et al. (https://github.com/peteboyd/lammps_interface) since it determines the hybridizations and identifies atom types corresponding to UFF, and then using that to re-generate a cif file which has unique atom names (e.g. C_3, C_R, C_R, C_R... from the original cif of just C, C, C, C...), from which I can then write the framework.def file of every unique grouping for bonds/angles/dihedrals/impropers.
Is there a better or more conventional way to do this than going through the hassle of using lammps_interface to do this?
Thanks in advance!
I have a question about utilizing flexible frameworks in a GCMC simulation in Raspa:
Is there an easy way to generate a cif which is labeled by atom types such that each atom type can be uniquely defined in bonds/angles/dihedrals/impropers a framework.def file? I hope to write my own framework.def file for UFF atom types, I see that there are some example framework.def files in the examples directory in the RASPA install, but they don't seem to have all the types in UFF e.g. C atoms in rings C_R.
One approach I was thinking of using was taking a cif -> lammps datafile generated from the lammps_interface from Boyd et al. (https://github.com/peteboyd/lammps_interface) since it determines the hybridizations and identifies atom types corresponding to UFF, and then using that to re-generate a cif file which has unique atom names (e.g. C_3, C_R, C_R, C_R... from the original cif of just C, C, C, C...), from which I can then write the framework.def file of every unique grouping for bonds/angles/dihedrals/impropers.
Is there a better or more conventional way to do this than going through the hassle of using lammps_interface to do this?
Thanks in advance!