Recent Posts

Pages: [1] 2 3 ... 10
Dear Pr. Dubbeldam,

I have a question on Widom's insertion. I noticed that the input file of the Raspa2 tutorial puts a pressure on Widom's insertion for Henry coefficient calculation. But after running some test at different pressure the results don't depend on the pressure and the partial pressure in the output file has an impossible value Partial pressure: -16605402.00000000000000 [Pa].

I just wanted confirmation that the pressure has no role in the actual code. And the algorithm is just making the random insertion of one gas molecule (if I set it to 1) in an empty framework which can be related to an adsorption constant at very low loading.

Thank you in advance for your time,

Best Regards,
General / Number of molecules in GEMC box
« Last post by pakamore on January 21, 2021, 01:20:12 PM »

I am trying to simulate molecule adsorption in MOFs using Gibbs ensemble MC algorithm. I was wondering how do you calculate the initial number of molecules in the box?

Kind regards,
Input files and parameters / Re: Flexible and chiral molecules
« Last post by bz475 on January 20, 2021, 05:54:35 PM »
Yes. There is a flexible ring in the molecule. I used a rigid/flexible model instead (the ring is fixed; the rest segments are flexible). Then the simulation went well! Thank you for your help.
Simulation algorithms and theory / Re: Simulated Annealing
« Last post by David Dubbeldam on January 19, 2021, 07:22:56 PM »
No, but you could achieve this with scripts. Just simulate at a certain temperature, and use the restart-file to restart at a lower temperature.
Note that force fields like 'GenericMOFs' are only examples (just like any molecule or structure file), just for the example cases in the code to work. For any real work you need to create and develop your own force fields, or take them from from the literature, and carefully construct, check and validate them.
Also, orthorhombic is much faster than triclinic. For triclinic structure, the distance computation is a matrix multiplication to get fractional coordinates, then apply periodic boundary conditions, and then convert back to Cartesian space.
It might be that if you choose the atomic positions wrong, that the molecules can overlap. This happened in particular with for example water where the larger oxygen shield the hydrogens. Often the hydrogens do not have a VDW parameter because the repulsion of the oxygen is sufficient. Choosing a wrong repulsion (too small sigma) leads to overlap with the hydrogens and hence numerical issues. So with classical force fields you should always be aware and avoid unphysical situations.
« Last post by joannewanghf on January 13, 2021, 06:53:12 AM »
I modified atom coordinates of C2H2 and problem solved. But I don't know why.
First of all you have to look at the number of adsorbate molecules. A monte carlo cycle in raspa is defined as min(20, N) where N is the number of adsorbate molecules. So if there are more molecules in the simulation cell than you simply have more moves per cycle.

Then you say, that computational expense of one cycle should scale approx. with N^2 because you have to evaluate the energies.

Does this help?
« Last post by joannewanghf on January 12, 2021, 07:14:15 AM »
Dear Prof. Dubbeldam and RASPA community,
I have used RASPA 2.0.37 for gas adsorption simulations in a Cu-MOF in last months.

I built myown forcefiled files based on Dubbeldam2012MIL-101, and got reasonable isotherm data for CH4 and CO2 adsorption. But encountered ENERGY DRIFT warning when I move to C2H2 (acetylene) adsorption, even at low pressure (e.g. 24Pa, 298K).

I found this warning would be eliminated when the charge of C_C2H2 and H_C2H2 equal to zero, but it leads to very low absolute adsorption (i.e., 0.02 cm^3/g. the experimental result is ~52 cm^3/g).  When I set the charge of C_C2H2 and H_C2H2 as 0.278, I got close adsorption as experiment but ENERGY DRIFT warning occurs.

I tried to change, respectively, radii of Cu, C_C2H2 and H_C2H2 in pseudoatom.def, L-J parameters of Cu, C_C2H2 and H_C2H2 in force_field_mixing_rules.def. All of attempts led to dramatically changes in amount of total ENERGY DRIFT and seems no rules. Besides, I performed two runs, respectively, with the same input files, it gives very different total energy drift.

So how can I fix this problem, and how to build a proper forcefield for specific systems, is there some guidelines or skills?

Some parameters used in one of my jobs with the smallest total energy drift (1.11544) is attached :
Pages: [1] 2 3 ... 10