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<div style="direction:ltr; font-family:Tahoma; color:#000000; font-size:10pt">Hello,
<div> 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. </div>
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<div>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.</div>
<div>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. </div>
<div>1. temparature coupling </div>
<div>2. Pressure coupling</div>
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<div>I want to ask that which coupling will be better for temperature; </div>
<div>a. Berendsen coupling</div>
<div>b. V-rescale coupling</div>
<div>c. nose-hoover coupling</div>
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<div>AND for pressure:</div>
<div>a. Berendsen coupling</div>
<div>b. Parrinello-Rahman coupling</div>
<div>c. Martyna-Tuckerman-Tobias-Klein implementation coupling</div>
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<div>I am also little confused over the pcoupltype, where options are isotropic; semi-isotropic and anisotropic.</div>
<div>Please help me in this matter.</div>
<div>Thanks in advance;</div>
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<div>With regards ...ANik</div>
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<div style="font-size:9pt; font-family:'Calibri',sans-serif">========================================================<br>
Anik Sen<br>
Student<br>
CSIR-Central Salt & Marine Chemicals Research Institute,<br>
Gijubhai Badheka Marg.<br>
Bhavnagar, Gujarat 364002<br>
<div><img alt="www.csmcri.org" src="http://www.csmcri.org/images/logo.png"></div>
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