<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:times new roman, new york, times, serif;font-size:12pt"><DIV></DIV>
<DIV>Thank you very much, Zhenhei.<BR> </DIV>Other Mails:<BR>chiloo7@hotmail.com<BR>chiloo777@gmail.com
<DIV style="FONT-SIZE: 12pt; FONT-FAMILY: times new roman, new york, times, serif"><BR><BR>
<DIV style="FONT-SIZE: 12pt; FONT-FAMILY: times new roman, new york, times, serif">----- Original Message ----<BR>From: Li Zhenhai <shibalagu.thu@gmail.com><BR>To: "gmx-users@gromacs.org" <gmx-users@gromacs.org><BR>Sent: Saturday, October 13, 2007 5:44:02 PM<BR>Subject: [gmx-users] Re: gmx-users Digest, Vol 42, Issue 50<BR><BR>Hello, chiloo,<BR><BR> Professor Xavier Periole told me a method to extract the energy of one composition.<BR><BR> You can follow what he/she said:<BR><BR>Message: 2<BR>Date: Thu, 11 Oct 2007 14:25:35 +0200<BR>From: "Xavier Periole" <<A href="mailto:X.Periole@rug.nl" ymailto="mailto:X.Periole@rug.nl">X.Periole@rug.nl</A>><BR>Subject: Re: [gmx-users] Calculating the energy of one molecule in the<BR> multi-molecule system<BR>To: Discussion list for GROMACS users <<A href="mailto:gmx-users@gromacs.org"
ymailto="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A>><BR>Message-ID: <<A href="mailto:web-56146831@mail3.rug.nl" ymailto="mailto:web-56146831@mail3.rug.nl">web-56146831@mail3.rug.nl</A>><BR>Content-Type: text/plain;charset=utf-8;format="flowed"<BR><BR><BR>To get the bonded energy terms of one molecule in your system you<BR>have to generate a trajectory file containing this molecule only:<BR><BR>trjconv -f full.trr -n molecule.ndx -o molecule.trr<BR><BR>and then rerun the simulation using a tpr containing only the topology<BR>of your molecule:<BR><BR>grompp -f molecule.mdp -c molecule.gro -o molecule.tpr<BR>mdrun -rerun molecule.trr -s molecule.tpr<BR><BR>Notes:<BR>1- you MUST use the a trr trajectory (full precision). the coordinates<BR>in xtc files are not precise enough.<BR>2- the molecule.mdp should be identical to the original one except<BR>for the update of the neighbor list (nstlist = 1) and print energies<BR>every step
(nstenergy).<BR><BR><BR>Li Zhenhai<BR>Department of Engineering Mechanics<BR>Tsinghua University<BR>Beijing 100084<BR>China<BR>Tel: 86-10-62773779<BR>E-mail: <A href="mailto:shibalagu.thu@gmail.com" ymailto="mailto:shibalagu.thu@gmail.com">shibalagu.thu@gmail.com</A><BR><BR>2007-10-13<BR><BR>======= 2007-10-13 18:00:07 您在来信中写道：=======<BR><BR>>Send gmx-users mailing list submissions to<BR>> <A href="mailto:gmx-users@gromacs.org" ymailto="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A><BR>><BR>>To subscribe or unsubscribe via the World Wide Web, visit<BR>> <A href="http://www.gromacs.org/mailman/listinfo/gmx-users" target=_blank>http://www.gromacs.org/mailman/listinfo/gmx-users </A><BR>>or, via email, send a message with subject or body 'help' to<BR>> <A href="mailto:gmx-users-request@gromacs.org"
ymailto="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</A><BR>><BR>>You can reach the person managing the list at<BR>> <A href="mailto:gmx-users-owner@gromacs.org" ymailto="mailto:gmx-users-owner@gromacs.org">gmx-users-owner@gromacs.org</A><BR>><BR>>When replying, please edit your Subject line so it is more specific<BR>>than "Re: Contents of gmx-users digest..."<BR>><BR>><BR>>Today's Topics:<BR>><BR>> 1. Energy of each composition (chiloo Laohpongspaisan)<BR>><BR>><BR>>----------------------------------------------------------------------<BR>><BR>>Message: 1<BR>>Date: Sat, 13 Oct 2007 01:02:08 -0700 (PDT)<BR>>From: chiloo Laohpongspaisan <<A href="mailto:chiloo77@yahoo.com" ymailto="mailto:chiloo77@yahoo.com">chiloo77@yahoo.com</A>><BR>>Subject: [gmx-users] Energy of each composition<BR>>To: <A href="mailto:gmx-users@gromacs.org"
ymailto="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A><BR>>Message-ID: <<A href="mailto:943314.93877.qm@web31602.mail.mud.yahoo.com" ymailto="mailto:943314.93877.qm@web31602.mail.mud.yahoo.com">943314.93877.qm@web31602.mail.mud.yahoo.com</A>><BR>>Content-Type: text/plain; charset="us-ascii"<BR>><BR>>Dear all, <BR>><BR>>Is there a tool of Gromacs extracing the energy of some composition in the system? <BR>>For example, there are protein, lipid , and water in my system, how can i investigate the energy of protein along the time? <BR>><BR>>Thanks in advance, <BR>>chiloo <BR>><BR>><BR>> <BR>>Other Mails:<BR>><A href="mailto:chiloo7@hotmail.com" ymailto="mailto:chiloo7@hotmail.com">chiloo7@hotmail.com</A><BR>><A href="mailto:chiloo777@gmail.com" ymailto="mailto:chiloo777@gmail.com">chiloo777@gmail.com</A><BR>><BR>><BR>>
<BR>>____________________________________________________________________________________<BR>>Pinpoint customers who are looking for what you sell. <BR>><A href="http://searchmarketing.yahoo.com/" target=_blank>http://searchmarketing.yahoo.com/ </A><BR>>-------------- next part --------------<BR>>An HTML attachment was scrubbed...<BR>>URL: <A href="http://www.gromacs.org/pipermail/gmx-users/attachments/20071013/3ec78183/attachment-0001.html" target=_blank>http://www.gromacs.org/pipermail/gmx-users/attachments/20071013/3ec78183/attachment-0001.html </A><BR>><BR>>------------------------------<BR>><BR>>_______________________________________________<BR>>gmx-users mailing list<BR>><A href="mailto:gmx-users@gromacs.org" ymailto="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A><BR>><A href="http://www.gromacs.org/mailman/listinfo/gmx-users" target=_blank>http://www.gromacs.org/mailman/listinfo/gmx-users
</A><BR>>Please search the archive at <A href="http://www.gromacs.org/search" target=_blank>http://www.gromacs.org/search</A> before posting!<BR>><BR>>End of gmx-users Digest, Vol 42, Issue 50<BR>>*****************************************<BR><BR>= = = = = = = = = = = = = = = = = = = =<BR><!-- kill -->
<DIV><BR><BR>-----Inline Attachment Follows-----<BR><BR>_______________________________________________<BR>gmx-users mailing list <A href="mailto:gmx-users@gromacs.org" ymailto="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A><BR><A href="http://www.gromacs.org/mailman/listinfo/gmx-users" target=_blank>http://www.gromacs.org/mailman/listinfo/gmx-users</A><BR>Please search the archive at <A href="http://www.gromacs.org/search" target=_blank>http://www.gromacs.org/search</A> before posting!<BR>Please don't post (un)subscribe requests to the list. Use the <BR>www interface or send it to <A href="mailto:gmx-users-request@gromacs.org" ymailto="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</A>.<BR>Can't post? Read <A href="http://www.gromacs.org/mailing_lists/users.php" target=_blank>http://www.gromacs.org/mailing_lists/users.php</A></DIV></DIV><BR></DIV></div><br>
<hr size=1>Fussy? Opinionated? Impossible to please? Perfect. <a href="http://us.rd.yahoo.com/evt=48516/*http://surveylink.yahoo.com/gmrs/yahoo_panel_invite.asp?a=7 ">Join Yahoo!'s user panel</a> and lay it on us.
</body></html>