[gmx-users] Pressure change after NPT equilibriation

[Justin A. Lemkul]

shilpa yadahalli wrote:
> Dear Justin,
> Thanks alot for your such a fast reply.
> I will surely go thr the page mentioned by you.
> Thanks-alot again.,
> 

Given this information, I still think everything is completely normal.

-Justin

> Here is my mpt.mdp file: ( i start from output of nvt equilibration).
> 
> ; Run parameters
> integrator    = md        ; leap-frog integrator
> nsteps    = 50000        ; 2 * 50000 = 100 ps
> dt        = 0.002        ; 2 fs
> ; Bond parameters
> continuation    = yes        ; Restarting after NVT
> constraint_algorithm = lincs    ; holonomic constraints
> constraints    = all-bonds    ; all bonds (even heavy atom-H bonds) 
> constrained
> lincs_iter    = 1        ; accuracy of LINCS
> lincs_order= 4        ; also related to accuracy
> ; Neighborsearching
> ns_type    = grid        ; search neighboring grid cells
> nstlist    = 5        ; 10 fs
> rlist        = 1.0        ; short-range neighborlist cutoff (in nm)
> rcoulomb    = 1.0        ; short-range electrostatic cutoff (in nm)
> rvdw        = 1.0        ; short-range van der Waals cutoff (in nm)
> ; Electrostatics
> coulombtype    = PME        ; Particle Mesh Ewald for long-range 
> electrostatics
> pme_order    = 4        ; cubic interpolation
> fourierspacing    = 0.16        ; grid spacing for FFT
> ; Temperature coupling is on
> tcoupl    = V-rescale    ; modified Berendsen thermostat
> tc-grps    = Protein Non-Protein    ; two coupling groups - more accurate
> tau_t    = 0.1    0.1    ; time constant, in ps
> ref_t        = 300     300    ; reference temperature, one for each 
> group, in K
> ; Pressure coupling is on
> pcoupl        = Parrinello-Rahman    ; Pressure coupling on in NPT
> pcoupltype    = isotropic    ; uniform scaling of box vectors
> tau_p        = 2.0        ; time constant, in ps
> ref_p        = 1.0        ; reference pressure, in bar
> compressibility = 4.5e-5    ; isothermal compressibility of water, bar^-1
> ; Periodic boundary conditions
> pbc        = xyz        ; 3-D PBC
> ; Dispersion correction
> DispCorr    = EnerPres    ; account for cut-off vdW scheme
> ; Velocity generation
> gen_vel        = no        ; Velocity generation is off
> ------------------------------------------------------------------------
> *From:* Justin A. Lemkul <jalemkul at vt.edu>
> *To:* shilpa yadahalli <shilpa_09honey at yahoo.com>; Discussion list for 
> GROMACS users <gmx-users at gromacs.org>
> *Sent:* Wednesday, November 16, 2011 12:02 AM
> *Subject:* Re: [gmx-users] Pressure change after NPT equilibriation
> 
> 
> 
> shilpa yadahalli wrote:
>  > After doing NPT simulation I plot pressure and density. How much 
> pressure change is considered as normal? I'm getting pressure change +/- 
> 500 bar, after doing NPT equilibration for most of my proteins. And for 
> one of the protein it is as high as +/- 1000 bar.
>  > Can anybody tell me what is the Normal/expected pressure change. My 
> temperature is constant 300 K. (I m running simulations at normal 
> conditions of temperature and pressure. 300K, 1 bar, using  _AMBER99SB_ 
> FF, protein is globular with 92 amino acids). Log file etc, does not 
> shows any warnings and simulation also does not show any inconsistent 
> topology shifts.
>  > After my production run also, i do not get any warnings. and my rmsd 
> is below 0.2.
>  > but i am not much happy with the pressure changing so much.
>  >
> 
> Sounds completely normal.
> 
> http://www.gromacs.org/Documentation/Terminology/Pressure
> 
> You haven't shown your .mdp settings so it's hard to gauge what you 
> should expect, but again, this is expected behavior for the reasons 
> described at the above link.
> 
> -Justin
> 
> -- ========================================
> 
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
> ========================================
> 
> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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