I usually use 1.0 for my systems and I get the correct values for the temperatures. If I couple it as a system, the low T-CNT yields a different value than the target 300K.
On Mon, Aug 19, 2013 at 11:48 AM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 8/19/13 11:42 AM, HANNIBAL LECTER 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 refcoord-scaling option doesn't matter with frozen groups. Anything > that is frozen, by definition, never has its position updated. Under the > influence of pressure coupling, other particles around the frozen group can > have their positions scaled and thus collide with the frozen group, which > has remained in its original location. > > > >> The outputs are from g_energy. >> >> > OK, good. > > > 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 >> > > Note that tau_t is the inverse friction constant, not the "normal" > coupling constant. In this case, I don't know what appropriate values are, > especially if one of your groups is restrained. The manual advises a value > of 2.0, so at least try that. Otherwise, try coupling the System as a > whole or use a different integrator (i.e., md) to try to figure out the > origin of the problem. > > -Justin > > 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 <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> >>> <htt**p://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<h**ttp://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. 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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? 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