I am performing NPT here but this artifact is independent of whether one is using NPT or NVT.
On Mon, Aug 19, 2013 at 11:42 AM, HANNIBAL LECTER < hanniballecte...@gmail.com> wrote: > Thanks Justin. > > I am not sure how it is fundamentally incompatible. Especially with > refcoord-scaling = com. Can you please provide with some more input on that? > > > The outputs are from g_energy. > > Here is the .mdp file. > > define = -DPOSRES_CNT > constraints = all-bonds > pbc = xyz > integrator = sd > ld_seed = 215546 > dt = 0.002 ; ps ! > nsteps = 50000 ; 50 ns > ;nsteps = 125000 ; 250 ps > nstcomm = 10 > nstcalcenergy = 10 > nstxout = 0 > nstxtcout = 5000 ;every 10 ps > nstvout = 100 > nstfout = 0 > nstlog = 1000 > nstenergy = 1000 > nstlist = 10 > ns_type = grid > rlist = 1.0 > vdwtype = cut-off > rvdw = 1.0 > coulombtype = pme > rcoulomb = 1.0 > fourierspacing = 0.12 > pme_order = 4 > ewald_rtol = 1e-5 > optimize_fft = yes > tc-grps = Protein CNT SOL > tau_t = 1.0 1.0 1.0 > ref_t = 300.000 300 300 > ;freezegrps = CNT > ;freezedim = Y Y Y > ; Energy monitoring > energygrps = CNT Protein SOL > ; energygrp-excl = CNT CNT > ; Isotropic pressure coupling is now on > Pcoupl = Berendsen > refcoord-scaling = com > Pcoupltype = isotropic > tau_p = 5 > compressibility = 4.5e-5 > ref_p = 1.0 > gen_vel = yes > gen_temp = 300.000 > gen_seed = 981487 > > > > On Mon, Aug 19, 2013 at 11:35 AM, Justin Lemkul <jalem...@vt.edu> wrote: > >> >> >> On 8/19/13 11:32 AM, HANNIBAL LECTER wrote: >> >>> Hi, >>> >>> I have been performing NPT simulations with CNT, Protein and water. >>> However, when I freeze the CNT, the system crashes with segmentation >>> fault. >>> >>> >> That is to be expected. Frozen atoms and pressure coupling are >> fundamentally incompatible. >> >> >> If I use position restraints, the temperature of the system is lower than >>> what it is expected to be. I am using sd coupling. >>> >>> If I couple the protein, CNT and SOL separately, the temperature of the >>> peptide is lower than 300K (~395K) while the temperature of the CNT is >>> 157K. The target temperature is 300K in all cases. Can any please explain >>> why such discrepancies are occurring? >>> >>> >> Are these temperatures from g_energy or g_traj? Can you please post a >> full .mdp file? >> >> -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 >> >> jalemkul@outerbanks.umaryland.**edu <jalem...@outerbanks.umaryland.edu>| >> (410) >> 706-7441 >> >> ==============================**==================== >> -- >> gmx-users mailing list gmx-users@gromacs.org >> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> >> * Please search the archive at http://www.gromacs.org/** >> Support/Mailing_Lists/Search<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<http://www.gromacs.org/Support/Mailing_Lists> >> > > -- 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
