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. 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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 <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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