[gmx-users] Pressure coupling in NPT equilibration step

[Justin Lemkul]

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


==========================================