problem solved. Many thanks, Hualin ________________________________________ From: [email protected] [[email protected]] On Behalf Of Justin A. Lemkul [[email protected]] Sent: Tuesday, September 27, 2011 2:46 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Center of mass: distance restrain for groups
Li, Hualin wrote: > Hi, Justin, > > Thank you very much for your reply. I use the following pull code in my > mdp file: > " > pull = umbrella > pull_geometry = distance > pull_dim = Y Y Y ;# 3D > pull_start = yes ;# add COM distance to initial value (initial value > = equilibrium value) > pull_ngroups = 1 ;# excluding the reference > pull_group0 = DPPC_DUPC_CHOL ;# the reference group - the membrane > pull_weights0 = 0 ;# use mass as weight > pull_pbcatom0 = -1 ;# or -1 - important for PBC of groups larger than > half box, > ;# as here for membrane (see manual) > pull_group1 = H4 ;# the protein > pull_weights1 = 0 ;# use mass as weight > pull_pbcatom1 = 0 ;# here is no issue since protein is smaller than half > the box > pull_rate1 = 0 ;# do not pull, just maintain distance! > pull_k1 = 50 ;# kJ mol^(-1) nm^(-2) > " > However , when I use grompp to pre-compile it , the error "Fatal error: > Number of weights (1) for pull group 0 'DPPC_DUPC_CHOL' does not match the > number of atoms (86016) > For more information and tips for troubleshooting, please check the GROMACS > website at http://www.gromacs.org/Documentation/Errors"; comes out. > > I change pull_weights0 to pull_weights0=86016, but it still doesn't > work. Could you please tell me the reason. > Thank you very much. > If you're not doing any special weighting, omit this keyword. -Justin > Best, > Hualin > > > > ________________________________________ > From: [email protected] [[email protected]] On Behalf > Of Justin A. Lemkul [[email protected]] > Sent: Monday, September 26, 2011 1:32 PM > To: Discussion list for GROMACS users > Subject: Re: [gmx-users] Center of mass: distance restrain for groups > > Justin A. Lemkul wrote: >> >> Li, Hualin wrote: >>> I am sorry about the last post, I mean "I am not sure about the word >>> "pull umbrella", is this command used in free energy >>> calculation to do the sampling ? I am not doing the free energy >>> calculation, should I change something in the mdp file to modify it >>> please? >>> >> Using "pull = geometry" simply applies a harmonic potential between the > > Sorry, that should read "pull = umbrella" :) > > -Justin > > -- > ======================================== > > 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 > -- ======================================== 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 -- 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
