thank you for your reply. because without the position restraint the cylindrical shape of my molecule (CNT)
changes. is it reasonble to use umbrella sampling along with the position restraint in y and z directions? ----- Original Message ----- From: Justin Lemkul <jalem...@vt.edu> To: Abed Askari <abedask...@yahoo.com>; Discussion list for GROMACS users <gmx-users@gromacs.org> Cc: Sent: Tuesday, August 20, 2013 12:42 AM Subject: Re: [gmx-users] regarding umbrella sampling On 8/19/13 4:03 PM, Abed Askari wrote: > Dear gmx-users > > I want to use umbrella sampling to calculate the PMF between > > two molecules and x-axis is the reaction coordinate. would you please > > tell me I can use position restraint in y and z directions for the pulling > group or not? > Why would you need to? In general, position restraints and an umbrella restraint are not simultaneously necessary. Sometimes they are, but usually not. -Justin -- ================================================== Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 ================================================== -- gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
