Thanks a lot. I could set up and perform the simulations using position restraints and md+nose-hoover thermostat as suggested by Justin. The combination seems to yield the correct canonical ensembles.
Equilibration with Berendsen barostat (with integrator=sd and refcoord-scaling = com) does not seem to have any problems. However, while performing simulations with parrinello-rahman barostat and refcoord-scaling=com using either sd or md, my system blows up. However, refcoord-scaling=all does not seem to have any issues. My position restraints are applied only to the CNT atoms and I am trying to simulate peptide near CNTs. All bonds are constrained in my simulations. Is there anything I am overlooking while moving from refcoord-scaling=com to refcoord-scaling=all? On Thu, Aug 22, 2013 at 6:20 AM, Mark Abraham <mark.j.abra...@gmail.com>wrote: > On Thu, Aug 22, 2013 at 12:51 AM, HANNIBAL LECTER > <hanniballecte...@gmail.com> wrote: > > 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. > > That may be true in the case where the non-interesting group is > unfrozen, but it does not follow that the perturbation to the > Hamiltonian from freezing the atoms (ie. that all interactions with > them now don't follow Newton's third law) is equally negligible. > > > 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. > > There's no heat flow at all to the frozen groups because they have no > velocity, so no temperature and no coupling. The atoms near the frozen > groups are going to be weird, and that has flow-on effects. Whether > those effects are significant is up to you to show, but you should > have a much easier time setting up a stable non-frozen CNT. Freezing a > group does not make your simulation appreciably faster. If I were to > review a paper that used freeze groups and made no attempt to show the > results were unaffected, then that paper would be on the fast track > for rejection... Relying on the thermostat to mask errors in the model > physics or the integration of it is similarly reprehensible, IMO. :-) > > Mark > > > 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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