[gmx-users] NPT Simulation average pressure lower than Reference set pressure

Agnivo Gosai agnivogromacs14 at gmail.com
Fri Oct 31 21:26:54 CET 2014

Dear Users

Dr. Micholas : Do you suggest that I do a longer run ? I am doing another
NPT carrying on from the previous NPT with a Parrinello-Rahman barostat. I
am attaching the NPT pressure and density plots , if anyone wants to have a
look at them.

Dr. Vitaly : I was thinking that my equilibration did not reach the
reference pressure because I need to do a longer run.

Tsjerk Wassenaar : Are you hinting at the running average for my pressure
plot ? I did not plot that. I was thinking of running a much longer
simulation and use a different barostat for another NPT simulation.

Dan Sponseller : I am also thinking of a much longer simulation using small
nstenergy value. My present value is 100.

To all : If you have any comment then please share.

My previous mail as reference :

Dear Users

I have a DNA-Protein system and I use AMBER99SB-Parmbsc0 ff in GROMACS
4.5.7 single precision. I use spc216 for solvation and TIP 3P water model.

My earlier work flow
1) Topology preparation
2) Box , Solvation and Ions
3) Energy minimization - Steepest descent ( converged after 1291 steps )
4) NVT equilibration using a V-rescale thermostat and ref temp = 300 K
 average temp = 299.7 K after 100 ps NVT sim. Total energy also constant
with minimal error.
5) Next is NPT sim ( with same thermostat on )

*Pressure Coupling part of npt.mdp file :*

; Pressure coupling is on
pcoupl              = Berendsen     ; Pressure coupling on in NPT, also
weak coupling
pcoupltype          = isotropic     ; uniform scaling of x-y-z box vectors
tau_p               = 2.0           ; time constant, in ps
ref_p               = 1.0           ; reference pressure (in bar)
compressibility     = 4.5e-5        ; isothermal compressibility, bar^-1
refcoord_scaling    = com

*g_energy output of npt.edr :*

A)​Statistics over 50001 steps [ 0.0000 through 100.0000 ps ], 1 data sets
All statistics are over 10001 points

Energy                      Average   Err.Est.       RMSD  Tot-Drift
Pressure                    -5.5706        6.2    84.8085    38.1219  (bar)

(B)All statistics are over 10001 points

Energy                      Average   Err.Est.       RMSD  Tot-Drift
Density                     1012.13       0.55    1.87172    3.17412

*My run parameters are :*
; Run parameters
integrator  = md                ; leap-frog integrator
nsteps      = 50000             ; 2 * 50000 = 100 ps
dt          = 0.002             ; 2 fs

My reference pressure is 1 bar , the average pressure is -5.5 bar . I
believe that the system failed to achieve the reference set pressure.

*So should I carry out the simulation for a longer time ?? Or should I use
a different barostat on the next NPT run or do it in a fresh NPT run.*

*Kindly suggest.*

Thanks & Regards
Agnivo Gosai
Grad Student, Iowa State University.

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