[gmx-users] NPT, freezegroups and Position Restraints.
hanniballecter13 at gmail.com
Mon Aug 19 17:47:16 CEST 2013
I am performing NPT here but this artifact is independent of whether one is
using NPT or NVT.
On Mon, Aug 19, 2013 at 11:42 AM, HANNIBAL LECTER <
hanniballecter13 at gmail.com> 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 outputs are from g_energy.
> 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
> 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:
>>> I have been performing NPT simulations with CNT, Protein and water.
>>> However, when I freeze the CNT, the system crashes with segmentation
>> 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 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)
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