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On 11/06/2012 2:43 PM, delara aghaie wrote:
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cite="mid:1339389793.6151.YahooMailNeo@web28705.mail.ir2.yahoo.com"
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<span style="font-weight: bold; font-family:
arial,helvetica,sans-serif;">Hello</span><br
style="font-weight: bold; font-family:
arial,helvetica,sans-serif;">
<span style="font-weight: bold; font-family:
arial,helvetica,sans-serif;">I want to make sure about the
command that I use. I have MD result for protein simulation MD
for 1 ns. I want to continue this simulation for longer time.
Check point file should be used for continuation:</span><br>
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<pre>grompp -f md.mdp -c md-out.gro -t md.cpt -p topol.top -o md_2.tpr
** md-out.gro is the latest coordinate file that I have after 1 ns MD
simulation
** md.cpt is the output of 1 ns simulation
<span style="font-family: arial,helvetica,sans-serif; font-weight: bold;">Is this command line enough to get the appropriate run input file for continuation?</span>
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Depends what your .mdp contains. See <a
href="http://www.gromacs.org/Documentation/How-tos/Extending_Simulations">http://www.gromacs.org/Documentation/How-tos/Extending_Simulations</a><br>
<br>
Mark<br>
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