<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"><br><div> </div>plz stop mailing me.....<br><div><div style="font-family: times new roman,new york,times,serif; font-size: 12pt;"><br><br><div style="font-family: times new roman,new york,times,serif; font-size: 12pt;">----- Original Message ----<br>From: Huey Ling Tan <huelyn@gmail.com><br>To: Discussion list for GROMACS users <gmx-users@gromacs.org><br>Sent: Wednesday, 14 November, 2007 11:23:01 PM<br>Subject: Re: [gmx-users] REMD As A Function of Distance Between 2 Chains<br><br>Dear all ,<br>thank you for those comments, we are aware of the paper. However, we are not sure how to implement the replica exchange in gromacs. We would like to run a set of replicas in which each replica corresponds to a different set of umbrella parameters. However, when setting
up a replica exchange run, all .tpr files use the same .ppa file so that each replica will have the same umbrella potential parameters. Do you know how to get around this problem.
<br>Thank you in advance,<br>Huey Ling <br><br><div><span class="gmail_quote">On 13/11/2007, <b class="gmail_sendername">Marcus Kubitzki</b> <<a rel="nofollow" ymailto="mailto:mkubitz@gwdg.de" target="_blank" href="mailto:mkubitz@gwdg.de">mkubitz@gwdg.de</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi Huey Ling,<br><br>have a look at Y.Sugita et al. J Chem Phys 113, 6042-6051 (2000) for<br>details on Hamiltonian REMD, especially the correct exchange criterion.<br>In their paper, they discuss in detail what you want to do, namely
<br>Replica Exchange Umbrella Sampling.<br><br>Marcus<br><br>Huey Ling Tan wrote:<br>> Hi all,<br>><br>> Is it feasible to do parallel tempering (replica exchange) as a function<br>> of distance with umbrella sampling applied?
<br>><br>> I can do REMD for a system containing 2 peptide chains as a function as<br>> temperatures, where I grompp each of the systems at different<br>> temperatures, and then gather the fullmd.tpr files in one folder with
<br>> the script I want for full md run.<br>><br>> But what if I want to do REMD as a function of distances (for example at<br>> 0.4, 0.6, 0.8, 1.0 nm between the chains, defined in the pull.ppa file),<br>> at a fixed temperature, with umbrella sampling applied? If this can be
<br>> done, how should I write the script for the full md run so that each of<br>> the pull.ppa files can recognise the system that it suppose to pull?<br>><br>> If anyone know how this can be done?<br>><br>
> Many thanks.<br>><br>> --<br>> Best regards,<br>> Huey Ling<br>><br>><br>> ------------------------------------------------------------------------<br>><br>> _______________________________________________
<br>> gmx-users mailing list <a rel="nofollow" ymailto="mailto:gmx-users@gromacs.org" target="_blank" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>> <a rel="nofollow" target="_blank" href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</a>
<br>> Please search the archive at <a rel="nofollow" target="_blank" href="http://www.gromacs.org/search">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 rel="nofollow" ymailto="mailto:gmx-users-request@gromacs.org" target="_blank" href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>> Can't post? Read <a rel="nofollow" target="_blank" href="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</a><br>
<br>--<br>Marcus Kubitzki<br>Max Planck Institute for Biophysical Chemistry<br>Computational Biomolecular Dynamics Group<br>Am Fassberg 11<br>D-37077 Göttingen<br>Germany<br>phone: ++49-551-2012312<br>fax: ++49-551-2012302
<br>Email: mkubitz[at]gwdg.de<br>www: <a rel="nofollow" target="_blank" href="http://www.mpibpc.mpg.de/groups/de_groot/">http://www.mpibpc.mpg.de/groups/de_groot/</a><br>_______________________________________________<br>gmx-users mailing list <a rel="nofollow" ymailto="mailto:gmx-users@gromacs.org" target="_blank" href="mailto:gmx-users@gromacs.org">
gmx-users@gromacs.org</a><br><a rel="nofollow" target="_blank" href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>Please search the archive at <a rel="nofollow" target="_blank" href="http://www.gromacs.org/search">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 rel="nofollow" ymailto="mailto:gmx-users-request@gromacs.org" target="_blank" href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>Can't post? Read
<a rel="nofollow" target="_blank" href="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</a><br></blockquote></div><br><br clear="all"><br>-- <br>Best regards,<br>Huey Ling
<!-- kill --><div><br><br>-----Inline Attachment Follows-----<br><br>_______________________________________________<br>gmx-users mailing list <a ymailto="mailto:gmx-users@gromacs.org" href="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 ymailto="mailto:gmx-users-request@gromacs.org" href="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></div><br>
<hr size=1>
For ideas on reducing your carbon footprint visit <a href="http://uk.promotions.yahoo.com/forgood/environment.html">Yahoo! For Good</a> this month.
</body></html>