Hi, Justin I am working with a triple helix using umbrella sampling method. When generating configurations, I pulled 1ns (md_pull.mdp). Then I got 15 configurations using 0.03 spacing. They are conf0.gro conf5.gro conf10.gro conf15.gro conf17.gro conf18.gro conf30.gro conf31.gro conf39.gro conf59.gro conf87.gro conf161.gro conf233.gro conf360.gro conf488.gro. Most of the configurations are within 0-100 frames. Does this affect the umbrella sampling simulations? Is there any pulling time requirement when generating the configurations? I was supposed to have a try and find the result, but found that the calculation is time-consuming. So I decided to ask you finally.
Thanks a lot, Ming -----Original Message----- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin Lemkul Sent: Wednesday, 18 March 2015 9:45 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] umbrella sampling tutorial On 3/17/15 9:06 PM, Ming Tang wrote: > Hi Justin, > > Thanks a lot. I can move forward now. > Recently, I am trying to pull a triple helix, and want to fix the center of > mass of the three terminal atoms. One paper said that it can be done by means > of a strong harmonic restrain with a super large spring constant in Gromos96 > 53 a6. But I still don't know how to do this. Can you give me some advice? Absolute restraints can be used in the pull code, but I've never done it. Note that such an approach is incompatible with NPT. Freezing may also be an option, but then you're acting directly on all the atoms and frozen groups carry their own artificiality. -Justin -- ================================================== Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul ================================================== -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
