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
[email protected]
+61 3 9903 9304
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble
a nail.
*From:* [email protected]
[mailto:[email protected]] *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
========================================
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