Thanks. I am not interested in the real physics of the freezegroups as I am assuming the fluctuations are negligible in the timescale of the fluctuations of the non-freeze groups. I thought that the langevin thermostat is quite effective in this case just to ensure that there is no net heat flow from the hot to the cold freeze groups. I maybe missing something.
On Wed, Aug 21, 2013 at 6:03 PM, Mark Abraham <mark.j.abra...@gmail.com>wrote: > On Wed, Aug 21, 2013 at 10:22 PM, HANNIBAL LECTER > <hanniballecte...@gmail.com> wrote: > > I am not sure what is the problem with using NPT, constraints and > > freezegroups. Unless there is some fundamental issue (which I cannot > think > > of) one should in principle be able to run NPT with the CNT system by > > freezing the CNT group. > > Frozen atoms do not have velocity, and the energy they would have > acquired in the update step is simply removed. So you get a > discontinuity every time step, because the new configuration did not > evolve from the previous one in a way that could mimic the statistics > of the ensemble with no frozen atoms. Also, there must be net flow of > heat if the temperature is constant in (even just) NVT, so you're not > modelling a normal ensemble at all. Constraints and box-size rescaling > in NPT make things worse. I can't imagine a use case (other than > equilibration of a problematic system) where you could use freeze > groups and believe you were modelling something like real physics. > > > I am using sd with LINCS to constraint the bonds. > > However, if md is used with SHAKE the system crashes with segmentation > > fault. Does anyone have any idea as to what could be the problem? > > Using freeze groups. > > Mark > > > On Mon, Aug 19, 2013 at 6:40 PM, HANNIBAL LECTER < > hanniballecte...@gmail.com > >> wrote: > > > >> Interestingly, removing position restraints does not have much of an > >> impact. > >> > >> > >> On Mon, Aug 19, 2013 at 1:40 PM, Justin Lemkul <jalem...@vt.edu> wrote: > >> > >>> > >>> > >>> On 8/19/13 11:58 AM, HANNIBAL LECTER wrote: > >>> > >>>> 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. > >>>> > >>>> > >>> What about changing the integrator to md? What happens if you remove > >>> restraints while using sd? > >>> > >>> -Justin > >>> > >>> > >>>> 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 <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> > >>>>>>> > > >>>>>>> <htt**p://lists.gromacs.org/**mailman/**listinfo/gmx-users< > http://lists.gromacs.org/mailman/**listinfo/gmx-users> > >>>>>>> <h**ttp://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/**<http://www.gromacs.org/Support/**> > >>>>>>> > >>>>>>> Mailing_Lists/Search<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> > >>>>>>> <http://**www.gromacs.org/**Support/**Mailing_Lists< > http://www.gromacs.org/**Support/Mailing_Lists> > >>>>>>> > > >>>>>>> <http://**www.gromacs.org/**Support/**Mailing_Lists< > http://www.gromacs.org/Support/**Mailing_Lists> > >>>>>>> <http:/**/www.gromacs.org/Support/**Mailing_Lists< > http://www.gromacs.org/Support/Mailing_Lists> > >>>>>>> > > >>>>>>> > >>>>>>>> > >>>>>>>> > >>>>>>> > >>>>>>> -- > >>>>> ==============================****==================== > >>>>> > >>>>> 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. 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> > >>>>> <http://**www.gromacs.org/Support/**Mailing_Lists< > http://www.gromacs.org/Support/Mailing_Lists> > >>>>> > > >>>>> > >>>>> > >>> -- > >>> ==============================**==================== > >>> > >>> 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? 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