[gmx-users] Pressure coupling in NPT equilibration step
mrshirts at gmail.com
Tue Dec 17 23:47:20 CET 2013
Note that Parrinello-Rahman contains some very minor approximations
(virial and kinetic energies off by 1/2 a step) that might affect
things by 0.3 atm. But that is almost certainly not the limiting
factor in the accuracy of the simulation.
On Mon, Dec 16, 2013 at 3:09 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> On Mon, Dec 16, 2013 at 2:42 PM, Mahboobeh Eslami <
> mahboobeh.eslami at yahoo.com> wrote:
>> hi GMX user
>> please help me
>> i want to study protein ligand complex by gromacs4.6.3. i repaired my
>> protein by MODELER and docked my ligand by AUTODOCK software.
>> i use amber99sb-ildn force field. after Energy Minimization i use
>> following option forTemperature coupling in NVT equilibration step:
>> ; Temperature coupling
>> tcoupl = v-rescale ; Couple temperature to external heat
>> bath according to velocity re-scale method
>> tc-grps = Protein_UNK NA_SOL ; two coupling groups - more accurate
>> tau_t = 0.1 0.1 ; Coupling time constant, controlling
>> strength of coupling
>> ref_t = 300 300 ; Temperature of heat bath
>> then i use following option for Pressure coupling in NPT equilibration
>> ; Pressure coupling
>> pcoupl = Parrinello-Rahman ; pressure coupling is on for
>> Pcoupltype = Isotropic ; uniform scaling of box
>> tau_p = 0.5 ; time constant, in ps
>> compressibility = 4.5e-5 ; isothermal compressibility
>> of water, bar^-1
>> ref_p = 1.0 ; reference pressure,
>> in bar
>> refcoord_scaling = com
>> i obtain temperature average 299.63 for NVT step bu i obtain pressure
>> average 1.35 for NPT stepI tried Various Thermostats and Barostatsbut i
>> don’t get good pressure averageClose to 1bar.
> You don't consider 1.35 bar close to 1 bar? For pressure, I'd call that
> exceptionally good, especially if you pay attention to the fluctuations.
> 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 | (410) 706-7441
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