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<DIV><FONT face=Arial size=2>Hello Mark,</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>tpbconv is also used to extend the simulation
run time.</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>try </FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>a) tpbconv -h</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>or</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>b) tpbconv -s original.tpr -f original.trr -e
original.edr. -o new.tpr -extend 750</FONT></DIV>
<DIV><FONT face=Arial size=2> </FONT></DIV>
<DIV><FONT face=Arial size=2>you will get new.tpr file. Use this new.tpr file
for the mdrun program for the continuation of your simulation till
1.5ns</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>Alok</FONT></DIV>
<BLOCKQUOTE
style="PADDING-RIGHT: 0px; PADDING-LEFT: 5px; MARGIN-LEFT: 5px; BORDER-LEFT: #000000 2px solid; MARGIN-RIGHT: 0px">
<DIV style="FONT: 10pt arial">----- Original Message ----- </DIV>
<DIV
style="BACKGROUND: #e4e4e4; FONT: 10pt arial; font-color: black"><B>From:</B>
<A title=mzottola@gmail.com href="mailto:mzottola@gmail.com">Mark Zottola</A>
</DIV>
<DIV style="FONT: 10pt arial"><B>To:</B> <A title=gmx-users@gromacs.org
href="mailto:gmx-users@gromacs.org">Discussion list for GROMACS users</A>
</DIV>
<DIV style="FONT: 10pt arial"><B>Sent:</B> Sunday, August 19, 2007 11:17
PM</DIV>
<DIV style="FONT: 10pt arial"><B>Subject:</B> Re: [gmx-users] Restart</DIV>
<DIV><BR></DIV>
<DIV>Dil,</DIV>
<DIV> </DIV>
<DIV>Thanks for the post. However, my original job was set for 750 ps
and ran successfully. Now, I would like to run an additional 750
ps. The tbpconv seems more for restarting after a crash or modifying the
original system. I only want to achieve a 1.5 ns simulation. So my
questions remain.</DIV>
<DIV> </DIV>
<DIV>Thanks,</DIV>
<DIV> </DIV>
<DIV> </DIV>
<DIV>Mark<BR><BR> </DIV>
<DIV><SPAN class=gmail_quote>On 8/19/07, <B class=gmail_sendername>Dilraj
Lama</B> <<A href="mailto:dennis@iitk.ac.in">dennis@iitk.ac.in</A>>
wrote:</SPAN>
<BLOCKQUOTE class=gmail_quote
style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid"><BR>>
I know this will get an rtfm response, however, I am writing this
after<BR>> looking at the online help pages and perusing the email
archive. <BR>><BR>> Simply put, I have a 750 ps simulation that I want
to run for another 750<BR>> ps. Is there a clear explanation
somewhere for how one should do this?<BR><BR>use tpbconv with -extend
option<BR><BR>> Specifically, if I shut off the gen_vel option in my mdp
file and use the <BR>> the "-t" option to specify my first trajectory
file are these the only<BR>> changes necessary? If I keep all
other options identical will I get the<BR>> 750<BR>> ps continuation I
desire?<BR><BR>There is no need to change the mdp file.Have a look at the
tpbconv options.<BR>><BR>> Thanks for the
help.<BR>><BR>><BR>> Mark<BR>>
_______________________________________________<BR>> gmx-users mailing
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Can't post? Read <A
href="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</A><BR><BR><BR>--<BR>Dilraj
Lama,<BR>Graduate student, <BR>Bioinformatics and Biomolecular Simualtion
lab,<BR>Dept. of BSBE;IITK-kanpur,<BR>Uttar pradesh,India-208016.<BR><A
href="mailto:email:dennis@iitk.ac.in">email:dennis@iitk.ac.in</A>,<A
href="mailto:dilraj2002@yahoo.com">
dilraj2002@yahoo.com</A><BR>mob:09415473973<BR><BR>_______________________________________________<BR>gmx-users
mailing list <A
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</A><BR></BLOCKQUOTE></DIV><BR>
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