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;
========================================================
Anik Sen
Student
CSIR-Central Salt & Marine Chemicals Research Institute,
Gijubhai Badheka Marg.
Bhavnagar, Gujarat 364002
[www.csmcri.org]
========================================================
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