No. The protein is probably not fixed in experiments. Erik
On 25 Nov 2014, at 12:55, WT Ren <rener...@gmail.com> wrote: > Justin： > Thanks for your reply, > so if I want to compare the results from simulation to experiment‘s， should > I fixed the reference group? > moreover， if I fixed the reference group，do I need to remove the > restriction on the center of mass motion? > > Weitong* Ren, PhD student* > Laboratory of Biophysics > Department of Physics > *Nanjing University* > Nanjing, Jiangsu, PR China > 210093 > tel : +86 025 8359 7226 > *wt...@biophy.nju.edu.cn <wt...@biophy.nju.edu.cn>* > > On Tue, Nov 25, 2014 at 8:31 PM, Justin Lemkul <jalem...@vt.edu> wrote: > >> >> >> On 11/25/14 3:33 AM, WT Ren wrote: >> >>> Dear all: >>> Recently, I'm using COM pulling to unfold a protein. So I'm >>> wondering how the gromacs deal with the reference group. Is the reference >>> group fixed, constrained or free? >>> >> >> Free, unless you do something to fix or restrain it. >> >> -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. -- 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.
