[gmx-developers] DNA MD problem

Mark Abraham Mark.Abraham at anu.edu.au
Mon Sep 17 09:02:26 CEST 2012

On 17/09/2012 4:21 PM, Anik Sen wrote:
> Hello,
>            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;

These are not questions about development of GROMACS. Please ask in the 
correct forum.

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