[gmx-users] Problem with coulombtype=user and 1,4 interactions

Dear Gromacs experts, I've been trying to use a tabulated potential for the coulombic-interactions with all Gromacs versions from 4.0.7 to 4.5.3. In combination with OPLS/AA force field and SPC/E water I used a potential by Gezelter for a simple system consisting of a protein in Water+Ions:

[gmx-users] Thermostating in NEMD

Hi, I was wondering how does a thermostat work in a Non Equilibrium Simulation(NEMD) in GROMACS. Does it subtract out the streaming velocity before applying the thermostat or does it not apply thermostat at all in the direction of the applied acceleration? Thanks. Apoorv Kalyankar Graduate Studen

Re: [gmx-users] Replica exchange

On 27/11/10 17:49, Sai Pooja wrote: Hi, I am running a script that uses mdrun of gromacs and does replica exchange (not using -replex). The reason is that I want to use different table files for different replicas. However, it seems that I cannot supply unique table names. For example, if I supp

Re: [gmx-users] Replica exchange

On 27/11/10 17:49, Sai Pooja wrote: Hi, I am running a script that uses mdrun of gromacs and does replica exchange (not using -replex). The reason is that I want to use different table files for different replicas. However, it seems that I cannot supply unique table names. For example, if I supp

[gmx-users] Replica exchange

Hi, I am running a script that uses mdrun of gromacs and does replica exchange (not using -replex). The reason is that I want to use different table files for different replicas. However, it seems that I cannot supply unique table names. For example, if I supply a table name different from table_P

Re: [gmx-users] Free Energy Calculation: dVpot/dlambda is always zero

Anirban Ghosh wrote: Hello Justin, Thanks a lot for the reply. Yes, I am using GROAMCS 4.5 and my system consists of two chains of two proteins, a substrate and an inhibitor solvated in water. So can you please tell me what should be the values for: couple-moltype The name of

[gmx-users] How to save the coordinates of all atoms in the 2D-arrays using xdrfile?

Dear gmxers, I am trying to perform an analysis on the trjectory file using xdrfile library. First of all, I want to save the coordinates of all atoms in three 2D-arrays, i.e. xx[step-1][natom-1], yy[step-1][natom-1], zz[step-1][natom-1]. How to do so? Could you give me some hints, please? If

[gmx-users] Re: HEME Charmm Force field in Gromacs format

Hi, You should install the 4.5.3 version of GROMACS which has support for heme (see gromacs homepage). Regards, Pär Bjelkmar 27 nov 2010 kl. 06.12 skrev shahid nayeem: > Hi > I am need of charmm27 forcefield in gromacs form. I am trying to simulate > heme protein which is bonded to MET S and