91
General / Re: Flexible-MOFs forcefield Issue
« Last post by Hattuck on January 02, 2020, 03:14:15 PM »Is there anywhere a list of all the interactions that you need to define for this to work?
Recent Posts
92
Input files and parameters / Error while using supercelled structure
« Last post by jeonghyeon on December 25, 2019, 09:34:18 AM »Dear Prof. Dubbeldam,
Currently, I am running raspa with ZIF-7 structure, which has triclinic unit cell.
When I conducted energy minimization and NPT MD simulations using this structure with 'UnitCell 1 1 1' command, the program gave me good results as I expected.
However, as I changed the UnitCell command from 1 1 1 to 1 1 2 or other supercelled one, the program was just stopped, and the reason was strange coulombic interaction energy.
When I compared the energy contributions summarized in the output file, all other energies were multiples of those of unitcell except for 'Host/Host Coulomb energy'.
Can you help me to solve this problem?
Best regards,
Jeong Hyeon.
Currently, I am running raspa with ZIF-7 structure, which has triclinic unit cell.
When I conducted energy minimization and NPT MD simulations using this structure with 'UnitCell 1 1 1' command, the program gave me good results as I expected.
However, as I changed the UnitCell command from 1 1 1 to 1 1 2 or other supercelled one, the program was just stopped, and the reason was strange coulombic interaction energy.
When I compared the energy contributions summarized in the output file, all other energies were multiples of those of unitcell except for 'Host/Host Coulomb energy'.
Can you help me to solve this problem?
Best regards,
Jeong Hyeon.
93
Simulation algorithms and theory / about CFCMC potential
« Last post by zhaoli2023 on December 20, 2019, 04:48:57 AM »Hi Professor Dubbeldam,
I wonder is there a specific reason why energies are capped when using CFC (in potentials.c, PotentialValue function)? Is that because CF energies are harder to evaluate than traditional LJ 12-6?
Thanks for your help!!!
I wonder is there a specific reason why energies are capped when using CFC (in potentials.c, PotentialValue function)? Is that because CF energies are harder to evaluate than traditional LJ 12-6?
Thanks for your help!!!
94
Output files / Re: Visualization of adsorption
« Last post by David Dubbeldam on December 09, 2019, 08:54:35 AM »You just import all the pdb- and cif-files you would like to visualize (so select multiple files during import).
Then you can set individual visualization properties, like origin, drawing-method, etc.
Then you can set individual visualization properties, like origin, drawing-method, etc.
95
Input files and parameters / Re: TraPPE-EH force field in molecule definitions
« Last post by David Dubbeldam on December 05, 2019, 04:28:53 PM »Either use a model that puts the charge-centers on the atomic centers (OPLS) or if the molecule is small you can also make the whole molecule rigid.
96
General / Re: Flexible-MOFs forcefield Issue
« Last post by YangLZ on November 15, 2019, 12:39:59 PM »Thanks for your response. 
97
General / Re: Flexible-MOFs forcefield Issue
« Last post by David Dubbeldam on November 08, 2019, 04:13:47 PM »For a force field for a flexible MOF you need to define all the interactions similar to the flexible IRMOF-1 example.
The GenericMOFs defines only the interactions of molecules with the framework.
The GenericMOFs defines only the interactions of molecules with the framework.
98
General / Flexible-MOFs forcefield Issue
« Last post by YangLZ on November 04, 2019, 03:03:52 PM »Dear Prof. Dubbeldam,
Is it OK to use the genericMOFs Forcefield to optimize a flexible-MOFs? Or every flexible-MOFs need a specific Forcefield, just like Dubbeldam2007FlexibleIRMOF-1 for IRMOF-1and Dubbeldam2007FlexibleIRMOF-10 for IRMOF-10?
Kind regards,
YangLZ
Is it OK to use the genericMOFs Forcefield to optimize a flexible-MOFs? Or every flexible-MOFs need a specific Forcefield, just like Dubbeldam2007FlexibleIRMOF-1 for IRMOF-1and Dubbeldam2007FlexibleIRMOF-10 for IRMOF-10?
Kind regards,
YangLZ
99
Input files and parameters / TraPPE-EH force field in molecule definitions
« Last post by GIV on October 23, 2019, 01:25:25 PM »Hello Prof. Dubbeldam,
I would like to use TraPPE – Explicit Hydrogen model to define a flexible di-n-propylamine molecule. For TraPPE-EH alkane models interaction sites for hydrogen are shifted from the atomic nuclei out to the C-H bond center. I would like to ask how can I set dummies in a molecule definition file?
Kind regards,
Ivan
I would like to use TraPPE – Explicit Hydrogen model to define a flexible di-n-propylamine molecule. For TraPPE-EH alkane models interaction sites for hydrogen are shifted from the atomic nuclei out to the C-H bond center. I would like to ask how can I set dummies in a molecule definition file?
Kind regards,
Ivan
100
Input files and parameters / Re: Charge equilibration for MOFs
« Last post by ignas on October 18, 2019, 11:57:45 AM »Hi,
thank you very much for your remark! So, in case when the number of framework atoms in output file and in cif do not match what could be done? As well, I noticed that program destroys the MOF connectivity in Framework_0_final_1_1_1.cif file. Only final P1 file contains proper connectivity.
thank you very much for your remark! So, in case when the number of framework atoms in output file and in cif do not match what could be done? As well, I noticed that program destroys the MOF connectivity in Framework_0_final_1_1_1.cif file. Only final P1 file contains proper connectivity.