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
