<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
<HTML><HEAD>
<META http-equiv=Content-Type content="text/html; charset=iso-8859-1">
<META content="MSHTML 6.00.2800.1479" name=GENERATOR>
<STYLE></STYLE>
</HEAD>
<BODY bgColor=#ffffff>
<DIV><FONT face=Arial size=2>
<DIV><FONT face=Arial size=2>Hi,</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>I am a new user of GROMACS. I am trying to run
MD simulation of one of the proteins. I followed the "getting started"
tutorial. My question is about minimization of my system in solvent.
According to the tutorial the minimization should be finished when either the
minimization has converged or a fixed number of steps has been performed. In my
case the minimization has converged before it reached the fixed number of steps.
But the potential energy after minimization IS NOT lower than
potential energy calculated by formula: -42(kJ/mole)xN (N is a number of SPC
water molecules). What is the problem? How can I fix it? The
same problem I had for Ribonuclease S-peptide given in
tutorial.</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>My second question is about short and full MD run.
According to the tutorial to generate the input for the position restrained
mdrun we have the following command:</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>grompp -f pr -o pr -c after_em -r after_em -p
speptide</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>for full md to do the same thing we have the
following command:</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>grompp -v -f full -o full -c after_pr -p
speptide</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>We can see that full MD is quite similar to
the restrained MD, but there is a difference which makes impossible to run full
MD without restrained MD. In full MD we have "-c after_pr" which is an input
file and "after_pr" can be obtained from short MD run. Is it correct that we
can't run full MD run without short MD or is there any other way to run
directly full MD (for example, use the same files for full MD as used for short
MD)?</FONT></DIV>
<DIV> </DIV>
<DIV><FONT face=Arial size=2>I look forward to hearing your reply,</FONT></DIV>
<DIV> </DIV>
<DIV><FONT face=Arial size=2>With best wishes,</FONT></DIV>
<DIV> </DIV>
<DIV><FONT face=Arial size=2>Gia
Maisuradze</FONT> </DIV></FONT></DIV></BODY></HTML>