[gmx-users] DNA MD PROBLEM

Anik Sen aniksen at csmcri.org
Mon Sep 17 19:06:18 CEST 2012

           This is Anik Sen from India. Am using Gromacs 4.5.5. to do some calculations on solvation and ligand binding interactions with DNA. I have some questions regarding the problem.

As water is present in the system, so according to the manual the define in the .mdp file must be -DFLEXIBLE. No probem in that.
But I read in different works by other people that for DNA they are using NPT ensemble. But there are two couplings in the .mdp file.
1. temparature coupling
2. Pressure coupling

I want to ask that which coupling will be better for temperature;
a.  Berendsen  coupling
b. V-rescale coupling
c. nose-hoover  coupling

AND for pressure:
a. Berendsen coupling
b. Parrinello-Rahman coupling
c. Martyna-Tuckerman-Tobias-Klein implementation coupling

I am also little confused over the pcoupltype, where options are isotropic; semi-isotropic and anisotropic.
Please help me in this matter.
Thanks in advance;

Anik Sen
CSIR-Central Salt & Marine Chemicals Research Institute,
Gijubhai Badheka Marg.
Bhavnagar, Gujarat 364002

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