[gmx-users] pressure coupling

[Justin Lemkul]

On 12/31/17 9:51 AM, kordzadeh at aut.ac.ir wrote:
> Hi all
>
> I want to investigate carbin nanotube as drug carrier I want to fnctionalize CNT and compare results with experimental but I have a problem
>
> functionalization performed in constant pressure 1 atm . Pressure in my system converges hard and I try several times I changed time step , number of steps and time constant but I didn't obtan a specific trend for pressure coupling. after 40 runs my best results is:
>
> Energy                      Average   Err.Est.       RMSD  Tot-Drift
> -------------------------------------------------------------------------------
> Pressure                    1.49409       0.63    295.065    2.01005  (bar)
>
>   

http://www.gromacs.org/Documentation/Terminology/Pressure

Your average pressure is 1.5 ± 295 bar. Ask yourself: is that in any way 
meaningfully different from a value of 1?

-Justin

>
> an example mdp file for npt is:
>   
>
> ; Pressure coupling is on
>
> pcoupl         = Parrinello-Rahman     ; Pressure coupling on in NPT
>
> pcoupltype         = isotropic             ; uniform scaling of box vectors
>
> tau_p         =  2             ; time constant, in ps
>
> ref_p         =  1.0             ; reference pressure, in bar
>
> compressibility     = 4.5e-5              ; isothermal compressibility of water, bar^-1
>
> what should I do?
>
> any suggest will be appreciated
>
> Thanks
>
> Azadeh
>

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

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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jalemkul at vt.edu | (540) 231-3129
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