[gmx-users] NPT, freezegroups and Position Restraints.
HANNIBAL LECTER
hanniballecter13 at gmail.com
Thu Aug 22 17:35:34 CEST 2013
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.abraham at gmail.com>wrote:
> On Thu, Aug 22, 2013 at 12:51 AM, HANNIBAL LECTER
> <hanniballecter13 at 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.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>|
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