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 <jalem...@vt.edu>
*To:* shilpa yadahalli <shilpa_09ho...@yahoo.com>; Discussion list for
GROMACS users <gmx-users@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
========================================
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