[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

[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

[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] 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

[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

[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.

[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] 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

[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

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

, the algorithm wants to connect molecules, which are not actually connected, and goes crazy, but it is just a guess. Dr. Vitaly V. Chaban On Mon, Jun 30, 2014 at 5:46 AM, Andy Chao ac...@energiaq.com wrote: Dear GROMACS users: I have a few questions about converting the .GRO files to .TOP files. I

[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 =

[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

[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