[gmx-users] NPT problem

[‪Mohammad Roostaie‬ ‪]

Hi Alex, Thank you for your reply.
By the term "results were good or not" I meant that whether the temperature, pressure, and density have converged to the preferred values or not (I mentioned it in the parenthesis, too).
I used "gmx x2top -f gr.gro -o topol1.top -ff cnt_oplsaa -name CNT -noparam -pbc" for generating the topology. then I used "gmx editconf -f grvmdn.pdb -o gr.gro -box 11 11 11 -angles 90 90 90" for creating the box then I filled it with water with "gmx solvate -cp gr.gro -cs spc216.gro -o gr_solv.gro -p topol.top" command. The x2top does not require the box dimensions. Should I use the "-pbc" option in editconf, too? Do you mean that first I should perform EM, NVT, NPT, and MD run on the graphene alone without water and any position restraints? Also, I followed the tutorial step by step. Also, I used it since this tutorial is mentioned on Gromacs website. Actually, I think that in this tutorial, the purpose is to generate a force filed for graphene based on OPLS force field. Moreover, I added the ffbonded.itp, ffnonbonded.itp, and tip3p.itp files from OPLS-AA force field to the directory for the water molecules. Also, after optimization of the graphene, I want to put a peptide inside the box, so I should add those files, also I think that I should add the aminoacids.rtp for the peptide in order to use a unique force field for all the molecules and not to use different force fields.
Kind regards,Mohammad



      From: Alex <nedomacho at gmail.com>
 To: Discussion list for GROMACS users <gmx-users at gromacs.org>; Mohammad Roostaie <mohammad.r0325 at yahoo.com> 
 Sent: Thursday, 13 July 2017, 22:51:48
 Subject: Re: [gmx-users] NPT problem
   
Also, that tutorial's parameters that are completely wrong for graphene. For bulk graphene bond types I suggest:
  CJ    CJ      1    0.14200   420420.0 

For bulk angles:
  CJ     CJ     CJ      1   120.000    659.346  

For bulk dihedrals:
  CJ     CJ     CJ     CJ      3     17.30770   0.00000 -17.30770   0.00000   0.00000   0.00000
These are parameters obtained from a Taylor-expanded optimized Tersoff-Brenner potential. Please count the number of bonds and dihedrals in your graphene model, as produced by x2top. If the number of dihedrals divided by the number of bonds gives you a number, say, equal to m, then multiply the dihedral parameters by that number. And do NOT use bond constraints -- you are simulating a crystal.
Alex
On Thu, Jul 13, 2017 at 10:45 AM, <mohammad.r0325 at yahoo.com> wrote:

Hi All GROMACS users,


 
I created graphene with nanotube modeler then I created a force field for graphene based on OPLS (by using this link and its parameters: http://chembytes.wikidot.com/ grocnt). I generated the topology file using x2top command. I put the graphene inside a box of water (TIP3P) which was larger than the graphene dimension with 1000  (kJ/mol nm^2) position restraint on all the atoms, and I performed the energy minimization and NVT equilibrations (in order to get an optimized structure of the graphene for further simulations). The results of both of them were good (energy level has reached a negative value with the order of 6 and the temperature has converged the preferred value). But, when I run the NPT equilibration, the results are not good (the pressure and density fluctuated very much and the averaged values are so far from the preferred ones). Also, during the NPT run, I received these messages:


step 53965: Water molecule starting at atom 127424 can not be settled.

Check for bad contacts and/or reduce the timestep if appropriate.

Wrote pdb files with previous and current coordinates


 
step 141454: Water molecule starting at atom 53366 can not be settled.

Check for bad contacts and/or reduce the timestep if appropriate.

Wrote pdb files with previous and current coordinates


 
step 141483: Water molecule starting at atom 53366 can not be settled.

Check for bad contacts and/or reduce the timestep if appropriate.

Wrote pdb files with previous and current coordinates


 
step 323815: Water molecule starting at atom 30509 can not be settled.

Check for bad contacts and/or reduce the timestep if appropriate.

Wrote pdb files with previous and current coordinates


 
step 323816: Water molecule starting at atom 30509 can not be settled.

Check for bad contacts and/or reduce the timestep if appropriate.

Wrote pdb files with previous and current coordinates


 
step 323818: Water molecule starting at atom 30509 can not be settled.

Check for bad contacts and/or reduce the timestep if appropriate.

Wrote pdb files with previous and current coordinates


 
step 355712: Water molecule starting at atom 121748 can not be settled.

Check for bad contacts and/or reduce the timestep if appropriate.

Wrote pdb files with previous and current coordinates


 
step 355714: Water molecule starting at atom 121748 can not be settled.

Check for bad contacts and/or reduce the timestep if appropriate.

Wrote pdb files with previous and current coordinates


 
step 355716: Water molecule starting at atom 121748 can not be settled.

Check for bad contacts and/or reduce the timestep if appropriate.

Wrote pdb files with previous and current coordinates


 
step 355718: Water molecule starting at atom 121748 can not be settled.

Check for bad contacts and/or reduce the timestep if appropriate.

Wrote pdb files with previous and current coordinates


 
step 469414: Water molecule starting at atom 101579 can not be settled.

Check for bad contacts and/or reduce the timestep if appropriate.

Wrote pdb files with previous and current coordinates


 
step 469416: Water molecule starting at atom 101579 can not be settled.

Check for bad contacts and/or reduce the timestep if appropriate.

Wrote pdb files with previous and current coordinates


 
step 469418: Water molecule starting at atom 101579 can not be settled.

Check for bad contacts and/or reduce the timestep if appropriate.

Wrote pdb files with previous and current coordinates


 
step 469420: Water molecule starting at atom 101579 can not be settled.

Check for bad contacts and/or reduce the timestep if appropriate.

Wrote pdb files with previous and current coordinates


 
, and a pdb file was saved after each step.
In addition, something interesting is that I performed another run with all of the previous parameters, except I did not put position restraint on the graphene, and the results of NPT were good and acceptable, and I did not get those messages.


Can you please help me figure this problem out? Since I should put the position restrain on the graphene. I really would appreciate any help.


If you need further information please let me know.
Kind regards,Mohammad
 

 
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