Hi, Check again the mdp options. Zero may not be the right choice for all of them
Mark On Thu, 15 Jun 2017 13:56 Linus Johannissen < linus.johannis...@manchester.ac.uk> wrote: > Thanks Justin, > > I'm using Gromacs 4.6.1. I don't think changing energygrps is going to > change anything as I have the same problem in the energy minimisation (zero > LJ (SR) and Coulomb (SR) energies). However, I found that if the simulation > seems to run fine if I use a cutoff of 999 instead of 0. To me that should > be the same, but is there any reason why I should not do that? > > Linus > ___________________ > Dr Linus Johannissen > Computational Chemistry Experimental Officer > Manchester Institute of Biotechnology > University of Manchester > UK > ________________________________________ > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [ > gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Justin > Lemkul [jalem...@vt.edu] > Sent: 14 June 2017 21:57 > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] In vacuo MD > > On 6/14/17 4:36 AM, Linus Johannissen wrote: > > I'm trying to run an in vacuo MD simulation using infinite non-bonding > cutoffs, but Gromacs doesn't seem to be calculating the non-bonding > interactions - the protein unfolds very rapidly and in the log file the LJ > (SR) and Coulomb (SR) values are 0. Does it look like there's something > wrong with my mdp file (below), or is it likely to be something else? > > > > This is how it should be done. Which version is this? Is there any > difference > if you specify "System" instead of "Protein" for the energygrps > (practically, > there shouldn't be, but you never know). > > -Justin > > > Thanks for your help > > Linus > > > > mdp file: > > > > title = Gas-phase protein simulation > > ; Run parameters > > integrator = md ; leap-frog integrator > > nsteps = 50000 ; 2 * 50000 = 100 ps > > dt = 0.001 ; 1 fs > > ; Output control > > nstxout = 0 ; suppress .trr output > > nstvout = 0 ; suppress .trr output > > nstenergy = 1000 ; save energies every 1 ps > > nstlog = 1000 ; update log file every 1 ps > > nstxtcout = 5000 ; write .xtc trajectory every 5 ps > > energygrps = Protein > > ; Bond parameters > > continuation = no ; first dynamics run > > constraint_algorithm = lincs ; holonomic constraints > > constraints = hbonds ; H-bonds constrained > > lincs_iter = 2 ; accuracy of LINCS > > lincs_order = 4 ; also related to accuracy > > > > comm-mode = angular > > > > ; OPTIONS FOR ELECTROSTATICS AND VDW > > cutoff-scheme = group > > vdw-type = Cutoff > > nstlist = 0 > > ns_type = simple > > pbc = no > > rlist = 0 > > coulombtype = cutoff > > rcoulomb-switch = 0 > > rcoulomb = 0 > > rvdw = 0 > > rvdw-switch = 0 > > > > ; Temperature coupling > > tcoupl = v-rescale ; modified Berendsen > thermostat > > tc-grps = Protein > > tau_t = 0.1 ; time constant, in ps > > ref_t = 300 ; reference temperature > > ; Pressure coupling > > pcoupl = no ; no pressure coupling in NVT > > ; Dispersion correction > > ; Velocity generation > > gen_vel = yes ; assign velocities from Maxwell distribution > > gen_temp = 300 ; temperature for Maxwell distribution > > gen_seed = -1 ; generate a random seed > > > > > > ___________________ > > Dr Linus Johannissen > > Computational Chemistry Experimental Officer > > Manchester Institute of Biotechnology > > University of Manchester > > UK > > > > -- > ================================================== > > 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.
