[gmx-users] Question about switching off non-bonded interactions between two molecules for MD simulation

[Alessandra Villa]

Hi,

As far as I understood, you have a protein and ligand (not covalently
bonded) and you want to switch off the interaction
between one aminoacid and the ligand.

Concerning approach 1,
If you have a merged topology (only one topology file with one [molecular
type] in your case  protein and ligand -  see pdb2gmx for more info)
[ exclusions] should working.
(see
http://manual.gromacs.org/current/reference-manual/topologies/molecule-definition.html?highlight=exclusion
)

Concerning approach 2,  you need only energygrp-excl  =  A B ( the group A
and B are already defined ) and you do not want to calculate the energy
between 2 groups
 ("energygrps"  group(s) for which to write short-ranged non-bonded
potential energies to the energy file)

Best regards
 Alessandra

On Wed, Nov 13, 2019 at 8:23 PM Soomin Choi <soominchoi777 at gmail.com> wrote:

> Dear GROMACS users,
>
> I am new to GROMACS software and have a question about switching off
> pair-wise non-bonded interactions between two molecules.
> I have a simulation box composed of a protein with a substrate inside the
> protein catalytic pocket and there are no covalent bonds between protein
> amino acids and a substrate. I would like to run MD simulation of this
> system after switching off non-bonded interactions between one of the amino
> acids and a substrate (leaving all intra non-bonded interactions & inter
> non-bonded interactions between given amino acids and other amino acids). I
> would appreciate it a lot if you could guide me on how to do this. Below
> are approaches I tried but got warning/error messages:
>
> Approach 1) use [exlucsions] in .top file
> If, let's say, atom # 1,2,3 are for the amino acid and atom# 4,5 is for a
> substrate, I added:
> [ exclusions]
> 1  4 5
> 2  4 5
> 3  4 5
> I have successfully obtained .tpr file from grompp but got a fatal error
> after mdrun:
> 'There is no domain decomposition for 448 ranks that is compatible with the
> given box and a minimum cell size of 25.3862 nm. Change the number of ranks
> or mdrun option -rdd or -dds'
>
> Approach 2) use energygrps and energygrp-excl in .mdp file
> If the name in the index for the amino acid and substrate is A and B
> respectively, I added:
> energygrps          = A B
> energygrp-excl      =  A B
> Also, I knew that energygrp-excl does not support Verlet cut-off scheme, I
> used a 'group'. However, I have got an error message when I used grompp:
> 'The sum of the two largest charge group radii (33.381752) is larger than
> rlist (1.200000)'
>
> Just to be clear below is a summary of my system:
> - a system composed of one protein and a small substrate
> - the substrate and amino acid that I would like to switch-off are charged
> (+1 and -1, respectively)
> - protein-substrate complex are solvated in TIP3P waters, total # of atoms
> in the system = ~450,000
>
> First of all, I am not sure whether these approaches are correct to
> switch-off non-bonded interactions between two molecules. Second, if so, I
> would like to know how to correct these issues.
>
> Sincerely,
>
> Soomin
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