On Mon, Dec 16, 2013 at 2:42 PM, Mahboobeh Eslami <
mahboobeh.esl...@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

jalem...@outerbanks.umaryland.edu | (410) 706-7441


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