[gmx-users] topology file

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

[gmx-users] EDLC simulation using Gromacs

Dear Users, Would you please suggest a few examples of using GROMACS to simulate an EDLC device? Thanks a lot! Andy -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.o

[gmx-users] Questions regarding converting .GRO files to .TOP files

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,

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 122, Issue 128

th.se/mailman/listinfo/gromacs.org_gmx-users or send >> 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

[gmx-users] TOP file conversion

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 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs

[gmx-users] Molecular Configuration of ionic liquids

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 -- Gromacs Users mailing list * Please search the

[gmx-users] GROMPP COMMAND

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 -

[gmx-users] mdrun error messages

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

[gmx-users] MDRUN error message

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

[gmx-users] illegal instruction while using mdrun command

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

[gmx-users] my log file to the mdrun error message that on Tue 15, July...

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

[gmx-users] mdrun error messages

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

[gmx-users] g_energy questions

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

[gmx-users] g_energy definition

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

[gmx-users] electrostatics forces and van der waals forces calculation

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 -- Gromacs Users mailing list * Please search th

[gmx-users] maximum energy in ipnic liquid

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 -- Gromacs Users

[gmx-users] g_tcaf

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

[gmx-users] How to modify the rtp file for graphene?

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

[gmx-users] g_tcaf error message

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