[gmx-users] Pressure coupling in NPT equilibration step

[Michael Shirts]

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
>> step
>>
>> ; Pressure coupling
>> pcoupl           = Parrinello-Rahman       ; pressure coupling is on for
>> NPT
>> Pcoupltype       = Isotropic                  ; uniform scaling of box
>> vectors
>> 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.
>
> http://www.gromacs.org/Documentation/Terminology/Pressure
>
> -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 | (410) 706-7441
>
>
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