[gmx-users] DNA MD PROBLEM

Justin Lemkul jalemkul at vt.edu
Mon Sep 17 19:35:18 CEST 2012

On 9/17/12 1:06 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.

There is no such statement in the manual.  In fact, -DFLEXIBLE should only be 
set during energy minimization if the convergence is not satisfactory.

> 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

Which algorithms do other people use in similar studies?  If they are not 
explicitly stated, contact the authors and ask them for more details, as their 
papers are incomplete.  Have you read the literature associated with all of 
these algorithms?  Do you know any deficiencies in these algorithms?  Many are 
discussed in the mailing list archive, especially for the Berendsen methods.

> I am also little confused over the pcoupltype, where options are isotropic; semi-isotropic and anisotropic.

For solutes in water, isotropic pressure coupling is appropriate.  For membranes 
or crystalline structures, the other two methods are often used.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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