Problem in the mdrun step for the system containing two parallel silica plates

User discussions
1

GROMACS version:gromacs/2018.6
GROMACS modification: Yes
Here post your question
I am trying to simulate a system containing two parallel silica plates in water (neutralized with Na+ ions). I am using topology file and mdp files generated by Charmm-gui in charmm36m force field. The energy minimization and two step equilibration (nvt followed by npt) has run well. But in my production run in nvt ensemble (nose-hoover barostat) with gromacs pull-code type “constraints” is not happening. In all the steps I have restrained the two plates. The warning are listed below:
WARNING: Listed nonbonded interaction between particles 1157 and 2812
at distance 15.652 which is larger than the table limit 2.288 nm.

This is likely either a 1,4 interaction, or a listed interaction inside
a smaller molecule you are decoupling during a free energy calculation.
Since interactions at distances beyond the table cannot be computed,
they are skipped until they are inside the table limit again. You will
only see this message once, even if it occurs for several interactions.

IMPORTANT: This should not happen in a stable simulation, so there is
probably something wrong with your system. Only change the table-extension
distance in the mdp file if you are really sure that is the reason.

I have tried with different gromacs version, by decreasing the step size from 2fs to 1fs and by changing the constraint algorithm from LINCS to SHAKE- but still the problem has not yet been solved. I think this is not due to the topology issue as previous equilibration has run well.

the pull code in my production mdp file is provided below:
;pull code
pull = yes
pull-ncoords = 1
pull-ngroups = 2
pull-group1-name = plate1
pull-group2-name = plate2
pull-coord1-type = constraint
pull-coord1-geometry = distance
pull-coord1-dim = N N Y
pull-coord1-groups = 1 2
pull-coord1-init = 0.5
pull-coord1-k = 1000
;
pull-print-com = yes
pull-print-ref-value = yes
pull-print-components = yes
pull-nstxout = 5000
pull-nstfout = 5000

Please help me with your suggestions. I am eagerly waiting for the solution.
Thanks in advance.

2

Hi,

I am working with a similar setup (water confined between silica walls); I don’t know the answer to your question, but nevertheless I have couple of observations:

  • how are you dealing with position restraints while doing npt equilibration? In my experience I’ve never managed to make the volume rescale work in this situation, since the COM of the two plates should be decoupled, but they are not (not in the current version of GROMACS), so maybe you want to double check that. Are you running a full channel or are there water-vapor interfaces? In the latter case npt may be skipped.

  • What are you using pull-code for? Is it to produce some a Couette flow (or other flows)? In that case there may be another (possibly simpler) alternative.

  • This is more of a curiosity: how does you substrate look like? I.e. is it crystalline or amorphous silica, or maybe a surrogate (e.g. quadrupoles)?