Recent Posts

Pages: 1 [2] 3 4 ... 10
11
You need a good force field to reproduce the correct occupancy. Also, the simulations are non-trivial and some people use parallel-tempering to compute the proper occupancy distributions.
12
General / Re: Flexible-MOFs forcefield Issue
« Last post by David Dubbeldam on January 16, 2020, 06:13:10 PM »
The interactions are up to you. Bond-potentials and bend-potentials between the atoms are common, but force fields differ in the treatment of torsion-and improper torsion potentials, and VDW and electrostatics.
13
Input files and parameters / Question on how to describe ions' chemical potential
« Last post by Haolong on January 09, 2020, 05:34:13 AM »
Hi, Professor David:

How can I describe ions' chemical potential instead of fugacity, which is mainly used to describe the property of gas, in the input file? :)

Kind regards,
Haolong
14
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?
15
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.
16
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!!!
17
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.
18
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.
19
General / Re: Flexible-MOFs forcefield Issue
« Last post by YangLZ on November 15, 2019, 12:39:59 PM »
Thanks for your response.  :)
20
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.
Pages: 1 [2] 3 4 ... 10