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
And where did "-box 11 11 11" come from? For pbc to work the box in your
case has to be a certain size corresponding to the graphene dimensions.
And no, it is not simply its approximate X-Y dimensions.
Alex
------------------------------------------------------------------------
*From:* Alex <nedoma...@gmail.com>
*To:* Discussion list for GROMACS users <gmx-us...@gromacs.org>;
Mohammad Roostaie <mohammad.r0...@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.r0...@yahoo.com
<mailto:mohammad.r0...@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
<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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