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<DIV><FONT face=Arial size=2>Hi Smith</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>If your run crashed, than you want to use the
original tpr. Tpbconv will start the next run, where the previous run crashed
(using of course the outputs from the crashed run), if the crash was due to
system powe failure for e.g. If the crash was due to MD system problems
(pressure scaling, box exploding ...) you have to see where the problem
is.</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>If you want to extend a previous run, with the same
mdp parameters, use -extend in tpbconv.</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>To continue a run, but with some parameters
changed, like tau_p, you have to create another tpr. The starting
coordinates will be the ones outputed by the previous run, in your case
run1.gro. But, at the final, in IMHO, I think you cannot analyse your traj as
run1+run2, cause you changed parameters. The "experimental" conditions are
not the same. Unless you want something else.</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>Think this commands will do the job:</FONT></DIV>
<DIV><FONT face=Arial size=2>grompp -f new.mdp -c run1.gro -o
new.tpr</FONT><BR>mdrun -v -s new.tpr</DIV>
<DIV><FONT face="Times New Roman" size=3></FONT> </DIV>
<DIV><FONT face=Arial size=2>If I'm incorrect, please correct me.</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>Regards,</FONT></DIV>
<DIV><FONT face=Arial size=2>Nuno</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV>######################################<BR>Nuno Ricardo Santos Loureiro da
Silva Ferreira<BR>Departamento de Química<BR>Faculdade de Ciências e
Tecnologia<BR>Universidade de Coimbra<BR>3004-535 Coimbra - Portugal<BR>Fax:
+351 239 827703 - <A
href="http://www.biolchem.qui.uc.pt">www.biolchem.qui.uc.pt</A><BR>########################################</DIV>
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<DIV style="FONT: 10pt arial">----- Original Message ----- </DIV>
<DIV
style="BACKGROUND: #e4e4e4; FONT: 10pt arial; font-color: black"><B>From:</B>
<A title=gsmith1@rediffmail.com
href="mailto:gsmith1@rediffmail.com">Gsmith1</A> </DIV>
<DIV style="FONT: 10pt arial"><B>To:</B> <A title=gmx-users@gromacs.org
href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A> </DIV>
<DIV style="FONT: 10pt arial"><B>Sent:</B> Tuesday, April 20, 2004 10:21
AM</DIV>
<DIV style="FONT: 10pt arial"><B>Subject:</B> [gmx-users] doubt</DIV>
<DIV><BR></DIV>
<P>dear gromacs users ,<BR>Iam a very new user to gromacs.I use
gromacs-3.2.1.I followed the exact steps given in getting started.html for
speptide.I have completed simulation of a protein for 2ns.I want to
continue(extend) the simulation for another 3ns and change tautp =1.0 in the
mdp file now.From archive mails i learned that tpbconv should be used as,<BR>I
got these outputs from first 2ns run run1.gro, run1.trr,run1.edr.but
<BR><BR>Iam confused which .tpr file i should use?<BR><BR>1.Can I use the .tpr
(created using grompp with afterminim.gro) for mdrun (first 2ns) or
should i use run1.gro file of just finished output of mdrun for 2ns for grompp
,change timesteps,other options ,create a new.tpr and then use this .tpr for
tpbconv as ,<BR><BR>*tpbconv -f run1.trr -s new.tpr -e run1.edr -o restart.tpr
-extend 3000<BR>*mdrun -v -s restart.tpr -o -e <BR><BR>Iam confused to which
tpr should i use.please anyone tell whats exact protocol.thanks
-smith </P><BR><BR><A
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