<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>Oh! Thanks a lot. </DIV>
<DIV>Samrat</DIV>
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<B><SPAN style="FONT-WEIGHT: bold">From:</SPAN></B> Justin A. Lemkul <jalemkul@vt.edu><BR><B><SPAN style="FONT-WEIGHT: bold">To:</SPAN></B> Discussion list for GROMACS users <gmx-users@gromacs.org><BR><B><SPAN style="FONT-WEIGHT: bold">Sent:</SPAN></B> Mon, November 15, 2010 6:16:51 PM<BR><B><SPAN style="FONT-WEIGHT: bold">Subject:</SPAN></B> Re: [gmx-users] compressing two selections or just the reverse of pulling simulation<BR></FONT><BR><BR><BR>Samrat Pal wrote:<BR>> Hi All,<BR>> In general what we do in pulling simulations that we pull one selection keeping the other fixed. In that case the distance between the two selections increases with time. Now, I want to push the selections i.e. one selection will be kept fixed and the other will be pushed towards the fixed one so that the distance between the two selection will decrease. Is it possible to do that in GROMACS? What should I modify in
the mdp file? I am attaching a mdp file that I have used for pulling simulations (only the pull part).<BR>> ; pull code<BR>> pull = umbrella<BR>> pull_geometry = distance<BR>> pull_dim = N N Y<BR>> pull_start = yes<BR>> pull_ngroups = 1<BR>> pull_group0 = freeze<BR>> pull_group1 = pull<BR>> pull_rate1 = 0.01<BR>> pull_k1 = 1000<BR>> I have used pull_dim N N Y as I am interested to pull only in the z direction. Should I just use N N -Y to do the compressing simulations?<BR>> <BR><BR>You can't specify "negative yes" for a pulling direction. Instead, just set the pull rate to, i.e., -0.01 to pull in the opposite direction.<BR><BR>-Justin<BR><BR>> Please suggest.<BR>> Thanks in advance.<BR>> Samrat<BR>> <BR><BR>-- ========================================<BR><BR>Justin A. Lemkul<BR>Ph.D. Candidate<BR>ICTAS Doctoral Scholar<BR>MILES-IGERT Trainee<BR>Department of
Biochemistry<BR>Virginia Tech<BR>Blacksburg, VA<BR>jalemkul[at]<A href="http://vt.edu/" target=_blank>vt.edu</A> | (540) 231-9080<BR>http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin<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>http://lists.gromacs.org/mailman/listinfo/gmx-users<BR>Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!<BR>Please don't post (un)subscribe requests to the list. Use the 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 http://www.gromacs.org/Support/Mailing_Lists<BR></DIV></DIV></div><br>
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