<DIV>David,</DIV>
<DIV> </DIV>
<DIV>Are there any options for continual run which supports in gromacs 3.1.1? or I need to change into 3.2.1 version only<BR></DIV>
<DIV>Best regards,</DIV>
<DIV>Chiloo</DIV>
<DIV><BR><B><I>David <spoel@xray.bmc.uu.se></I></B> wrote:</DIV>
<BLOCKQUOTE class=replbq style="PADDING-LEFT: 5px; MARGIN-LEFT: 5px; BORDER-LEFT: #1010ff 2px solid">On Sun, 2005-08-07 at 23:20 -0700, chiloo Laohpongspaisan wrote:<BR>> Dear All,<BR>> <BR>> How can i countinue the running of next MD with the last configuration<BR>> of previous MD (i use the Gromacs version 3.1.1). if I ran MD 1000 ps<BR>> already, and i'd like to run more 1000 ps with the last configuration<BR>> of the previous MD (so, the last configuration (.gro file )at 1000ps<BR>> of the previous MD is the same as the 1st configuration at 0 ps of the<BR>> next MD, that's right?)<BR>tpbconv -f -s -o -until 2000<BR>maybe you should add -e as well if that's supported in 3.2.1<BR><BR>> <BR>> I tried to use normal step to run the next MD, but the velocity seems<BR>> not to be the same.<BR>> this is my brief procedure:<BR>> -extract the configuration at 1000 ps of previous MD: trjconv -f<BR>> traj.trr -s md.tpr -o md-1000.gro -b 1000<BR>>
-use grompp to prepare the new file.tpr: grompp -f md.mdp -c<BR>> md-1000.gro -p top.top -o md2.tpr<BR>> -run MD: mdrun -s md2.tpr -o traj.trr -c pmd2.gro -g md2.log -e<BR>> md2.edr &<BR>> Please check it for me, what's wrong ?<BR>> <BR>> Best regards,<BR>> Chiloo<BR>> <BR>> <BR>> <BR>> __________________________________________________<BR>> Do You Yahoo!?<BR>> Tired of spam? Yahoo! Mail has the best spam protection around <BR>> http://mail.yahoo.com <BR>> <BR>> _______________________________________________<BR>> gmx-users mailing list<BR>> gmx-users@gromacs.org<BR>> http://www.gromacs.org/mailman/listinfo/gmx-users<BR>> Please don't post (un)subscribe requests to the list. Use the <BR>> www interface or send it to gmx-users-request@gromacs.org.<BR>-- <BR>David.<BR>________________________________________________________________________<BR>David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,<BR>Dept.
of Cell and Molecular Biology, Uppsala University.<BR>Husargatan 3, Box 596, 75124 Uppsala, Sweden<BR>phone: 46 18 471 4205 fax: 46 18 511 755<BR>spoel@xray.bmc.uu.se spoel@gromacs.org http://xray.bmc.uu.se/~spoel<BR>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++<BR><BR>_______________________________________________<BR>gmx-users mailing list<BR>gmx-users@gromacs.org<BR>http://www.gromacs.org/mailman/listinfo/gmx-users<BR>Please don't post (un)subscribe requests to the list. Use the <BR>www interface or send it to gmx-users-request@gromacs.org.<BR></BLOCKQUOTE><p>__________________________________________________<br>Do You Yahoo!?<br>Tired of spam? Yahoo! Mail has the best spam protection around <br>http://mail.yahoo.com