[gmx-users] Fw: Pressure coupling in NPT equilibration step

Mahboobeh Eslami mahboobeh.eslami at yahoo.com
Mon Dec 16 20:45:20 CET 2013

On Monday, December 16, 2013 11:12 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 Barostats but i don’t get good pressure average Close to 1bar.
please help me 
thanks a lot

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