Dear GROMACS Users:
I tried to use the g_tcaf command to calculate the viscosity of the ionic
liquid. I got the following error message while using the following
command:
g_tcaf -f NPT.trr -s NPT.tpr -n index.ndx -o tcaf.xvg
The error message is the following:
trn version: GMX_trn_file (single
Dear GROMACS Users:
I would like to simulate the graphene-electrode based electric double layer
capacitor device. I need to convert the .gro file to .top file by using
the g_x2top command. The command that I used is the following:
g_x2top -f device1.gro -ff oplsaa -o device1.top
My question i
Dear GROMACS Users:
I would like to use the g_tcaf command to compute the viscosity of ionic
liquid. I found out (searched online) that the g_tcaf command has some
problems. I used the following command
g_tcaf -f traj.trr -s NPT.tpr -n index.ndx -oa tcaf.xvg
But got error messages. Does anybod
Dear gromacs users:
is there any gromacs command that can allow us to compute the maximum
allowable energy that can be sustained on an ionic liquid structure?
in other words, instead of energy minimization, we would like to
compute maximum energy under stability.
Thanks!
Andy
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Gromacs Users
Dear GROMACS Users:
Would you please let me know how to calculate/extract the electrostatic
forces and van der waals forces of an ionic liquid structure in GROMACS?
Which GROMACS command should I use? g_enemat? g_potential?
Thanks a lot!
Andy
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Dear GROMACS USERS:
Thanks a lot for your supports and help! I would like to ask more
questions related to the output (*.xvg) of the command g_energy.
1. GROMACS computes the potential energy of an ionic liquid to be negative
beyond a specific time. What does negative energy of an ionic liquid
Dear GROMACS Users:
I would like to use the command g_energy to calculate the total free energy
of an electrolyte. I use the following command:
g_energy -f NPT.edr -s NPT.tpr -b 0 -e 1000 -o energy.xvg
GROMACS4.6.5 printed out the following:
Select the terms you want from the following list b
Dear GROMACS Users:
As I mentioned, I got the following log file when I used the "mdrun"
command. I installed GROMACS on my virtual machine. Is there any solution
to this problem?
Thanks!
Andy
PLEASE READ AND CITE THE FOLLOWING REFERENCE
H. J. C. Berendsen, D. van der Spoel and R. v
Dear GROMACS Users:
Here is my log file..
Please let me know how to fix this problem.
Thanks!
Andy
Log file opened on Tue Jul 15 21:01:52 2014
Host: server-Virtual-Machine pid: 10019 nodeid: 0 nnodes: 1
Gromacs version:VERSION 4.6.5
Precision: single
Memory model: 32 bit
Dear GROMACS Users:
I used the C4mimNTf2 ionic liquid TOP and GRO files to run MD simulation.
Here are the commands that I used:
grompp -f em.mdp -c C4mimNTf2.gro -p c4mimNTf2.top -o NPT.tpr
mdrun -v -deffnm NPT
I got the following error messages:
Reading file NPT.tpr Version 4.6.5 (single pr
Dear GROMACS Users:
I used the grompp command to run energy minimization of an ionic liquid
structure according to the following command:
grompp -f em.mdp -c C4mimNTf2.gro -p C4mimNTf2.top -o NPT.tpr
and then run molecular dynamics simulation as the following:
mdrun -s NPT.tpr -o NPT.trr
when
Dear GROMACS Users:
I used the grompp command to run energy minimization of an ionic liquid
structure according to the following command:
grompp -f em.mdp -c C4mimNTf2.gro -p C4mimNTf2.top -o NPT.tpr
and then run molecular dynamics simulation as the following:
mdrun -s NPT.tpr -o NPT.trr
when
Dear GROMACS Users:
I have a question regarding using the GROMPP command..
I first used the g_x2top command to convert the *.gro file of a graphene
sheet to the *.top file of the graphene sheet by using the forcefield.itp
file in the OPLSAA file folder as the following:
g_x2top -f graphene.gro -
Dear GROMACS Users:
Is there any software tool/program that allows one to construct the
molecular configuration of any ionic liquid? As a result, the software
program would generate the PDB or GRO file that can be used in GROMACS?
Thanks!
Andy
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Dear GROMACS Users:
I would like to convert a GRO file to the TOP file. Is it a better way to
use
pdb2gmx -f device.gro -p device.top
or to use
g_x2top -f device.gro -ff oplsaa -o device.top?
Thanks a lot!
Andy
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>> a mail to gmx-users-requ...@gromacs.org.
>
>
> --
>
> Message: 3
> Date: Mon, 30 Jun 2014 12:10:35 +0200
> From: "Dr. Vitaly Chaban"
> To: gmx-us...@gromacs.org
> Subject: Re: [g
Dear GROMACS users:
I have a few questions about converting the .GRO files to .TOP files. I
first used Python to create a sheet of graphene layer by using the
following Python codes:
from ase import *
from ase.structure import graphene_nanoribbon
from ase io.import*
gnr1 = graphene_nanoribbon(8,
Dear Users,
Would you please suggest a few examples of using GROMACS to simulate an
EDLC device?
Thanks a lot!
Andy
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Hi,
I have a few technical questions regarding creating the topology file by
using the command "g_x2top".
I would like to use the following GROMACS's command:
g_x2top -f device.gro -ff oplsaa -o device.top
to convert the .gro file to .top.
The problem that I have is that the force field for ca
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