AMBER Archive (2008)

Subject: AMBER: peptide at the box center during NVT-MD

From: Darek Czapiewski (darkcz_at_o2.pl)
Date: Mon May 26 2008 - 05:01:45 CDT

 Hi!
 
 I would like to keep my peptide at the box center during the NVT-MD simulation. Well, what should I do?
 
 If I use NTR=1 (together with a value RESTRAINT_WT of course), it will not be sufficient, because as the box becomes smaller (as a result of pressure), the distance from the top box border to the peptide axis gets another value as the distance from the bottom box border to the peptide axis. Initially, after the NPT-MD my peptide was at the center of the simulated box of course.
 
 
 
 Thank you in advance
 
 Darius

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