[gmx-users] NPT, freezegroups and Position Restraints.
HANNIBAL LECTER
hanniballecter13 at gmail.com
Thu Aug 22 00:51:31 CEST 2013
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.abraham at gmail.com>wrote:
> On Wed, Aug 21, 2013 at 10:22 PM, HANNIBAL LECTER
> <hanniballecter13 at 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 <
> hanniballecter13 at 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 <jalemkul at 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 <jalemkul at 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 <jalemkul at 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 at outerbanks.umaryland.******edu <jalemkul at outerbanks.**
> >>>>>>> umaryland.edu <jalemkul at outerbanks.**umaryland.edu<
> jalemkul at outerbanks.umaryland.edu>>>
> >>>>>>> | (410)
> >>>>>>> 706-7441
> >>>>>>>
> >>>>>>> ==============================******====================
> >>>>>>>
> >>>>>>>
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> >>>>>>> --
> >>>>> ==============================****====================
> >>>>>
> >>>>> 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 at outerbanks.umaryland.****edu <jalemkul at outerbanks.**
> >>>>> umaryland.edu <jalemkul at outerbanks.umaryland.edu>> | (410)
> >>>>> 706-7441
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> >>> --
> >>> ==============================**====================
> >>>
> >>> 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 at outerbanks.umaryland.**edu <jalemkul at outerbanks.umaryland.edu>|
> (410)
> >>> 706-7441
> >>>
> >>> ==============================**====================
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