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<DIV><BR>Thank you for your advice. </DIV>
<DIV>Yes, I thought about making series of runs with different forces for
restraints.</DIV>
<DIV>I wonder if restarting from trr files gives me perfect continuation
for the runs.</DIV>
<DIV> </DIV>
<DIV> </DIV>
<DIV>Michal</DIV>
<DIV> </DIV>
<DIV> <BR></o:p></SPAN></DIV></FONT></FONT>
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<DIV><BR>><I> Hello all.<BR></I>><I> <BR></I>><I> I wonder is there a
way for turning off the distance restraints during <BR></I>><I> the md
simulation.<BR></I>><I> I’m currently investigation different binding modes
of a small<BR></I>><I> ligand inside the active site of the receptor protein.
<BR></I>><I> I use restraints to force a proper orientation of
ligand<BR></I>><I> inside the active site during the first stages of the
simulation.<BR></I>><I> Then I would like to slowly turn off the restraints
between protein and </DIV></I>><I> small<BR></I>><I> molecule (without a
rapid change in distance restraints force) to<BR></I>><I> investigate the
complex stability. <BR></I>><I> Maybe someone knows how to
implement<BR></I>><I> it in Gromacs code? Please give me some
advice.<BR></I><BR>You could do it in a stepwise fashion, varying the .top file
only for <BR>successive restarts, rather than tweaking with the C
code.<BR><BR>Mark<BR></FONT></BODY></HTML>