Oh! Thanks a lot. Samrat
________________________________ From: Justin A. Lemkul <[email protected]> To: Discussion list for GROMACS users <[email protected]> Sent: Mon, November 15, 2010 6:16:51 PM Subject: Re: [gmx-users] compressing two selections or just the reverse of pulling simulation Samrat Pal wrote: > Hi All, > 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). > ; pull code > pull = umbrella > pull_geometry = distance > pull_dim = N N Y > pull_start = yes > pull_ngroups = 1 > pull_group0 = freeze > pull_group1 = pull > pull_rate1 = 0.01 > pull_k1 = 1000 > 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? > 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. -Justin > Please suggest. > Thanks in advance. > Samrat > -- ======================================== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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