<HTML><BODY>
<DIV><BR>In God We Trust<BR>Hello Dear Vaibhav Saraf <BR> > My
system consists of the protein, water of crystallization and<BR>>
additional water molecules. And before doing the position restraint<BR>>
MD, I wish to perform energy minimization once with the protein and<BR>>
its water of crystallization fixed and only the additional water<BR>>
molecules free. Later would do it un-restrained.<BR>> So need guidance on
whether I can fix the protein (along with its<BR>> water of
crystallisation) during energy minimization</DIV>
<DIV> </DIV>
<DIV>you can make an index file and make a fix group consists of
number of protein and water of crystallisation and then in mdp file define
freezegrps and freezedim ( Y Y Y ) and with MD integrator.</DIV>
<DIV><BR>Yours truly <BR>Karim Mahnam<BR>Institute of
Biochemistry and Biophysics (IBB)<BR>Tehran University <BR>
P.O.box 13145-1384<BR>Tehran <BR>Iran <BR><A href="http://www.ibb.ut.ac.ir/">
http://www.ibb.ut.ac.ir/</A></DIV>
<DIV><BR> </DIV>
</BODY></HTML>