[gmx-users] Pressure estimation from NVT

[Justin A. Lemkul]

Dallas Warren wrote:
> Have you looked at the data from which you calculated the pressure 
> average from?
> 

Very important point.  There was a bug in pressure-related output in Gromacs 
versions up to, and including 4.5.3.  The instantaneous values are correct, but 
the averages are flawed.

-Justin

> 
> Catch ya,
> 
> Dr. Dallas Warren
> 
> Medicinal Chemistry and Drug Action
> 
> Monash Institute of Pharmaceutical Sciences, Monash University
> 381 Royal Parade, Parkville VIC 3010
> dallas.warren at monash.edu
> 
> +61 3 9903 9304
> ---------------------------------
> When the only tool you own is a hammer, every problem begins to resemble 
> a nail.
> 
>  
> 
> *From:* gmx-users-bounces at gromacs.org 
> [mailto:gmx-users-bounces at gromacs.org] *On Behalf Of *Sikandar Mashayak
> *Sent:* Tuesday, 27 September 2011 3:48 AM
> *To:* Discussion list for GROMACS users
> *Subject:* [gmx-users] Pressure estimation from NVT
> 
>  
> 
> Hi
> 
> I am trying to determine pressure of water at given density and 
> temperature using SPC/E water model. To achieve this, I am doing NVT 
> bulk simulations and then using g_energy I get average pressure values. 
> The question I have is how accurate these average pressure predictions are?
> 
> e.g. I get average pressure of 185 bar for 300 K and 1 g/cm^3 water 
> density, but theoretical value for it is around 1 bar. What are the 
> possible reasons for this much deviation from theoretical value? Is 
> there anything wrong with my set up? I am using 2141 water molecules in 
> 4*4*4 periodic box, Nose-Hoover thermostat with 0.2ps time constant , MD 
> algorithm with 1fs time-step, LJ with 1.5 nm cut off and PME for 
> electrostatics.
> 
> thanks
> sikandar
> 

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

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

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