Sikandar Mashayak wrote:
Hi
@ Dallas and Justin
Do you mean that for gromacs version 4.5.3 averages computed using
g_energy may be flawed? And are you suggesting to compute average
Not "may be" - they are. There was a bug:
http://redmine.gromacs.org/issues/696
pressure explicitly from instantaneous P values in trajectory?
Upgrade to version 4.5.4 - there's nothing wrong with the values stored in the
.edr file, just the analysis of them. It's more accurate to use the .edr file
since it has a complete energy history.
@ Mark
Thanks for suggestion. I am doing 500 ps of equilibration and 10 ns of
production runs with 2141 molecules.
So the important point that I want to understand is that if I use the
right averaging or newer gromacs version, and do large system with
longer production runs, how accurate is the estimate of pressure values
from bulk water NVT simulations?
Pressure is an incredibly fickle quantity. See the extensive discussions in the
list archive about the ability to obtain proper values and their statistical
interpretation. It's been discussed countless times, even very recently.
-Justin
thanks
sikandar
On Mon, Sep 26, 2011 at 8:51 PM, Mark Abraham <mark.abra...@anu.edu.au
<mailto:mark.abra...@anu.edu.au>> wrote:
On 27/09/2011 3:48 AM, Sikandar Mashayak wrote:
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.
The length of your simulation, and the absence of the equilibration
period from your data collection are also critical factors in
obtaining accurate converged averages, but usually neglected when
people report what might be anomalies... please see
http://www.gromacs.org/__Documentation/Terminology/__Pressure
<http://www.gromacs.org/Documentation/Terminology/Pressure>
Mark
--
gmx-users mailing list gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>
http://lists.gromacs.org/__mailman/listinfo/gmx-users
<http://lists.gromacs.org/mailman/listinfo/gmx-users>
Please search the archive at
http://www.gromacs.org/__Support/Mailing_Lists/Search
<http://www.gromacs.org/Support/Mailing_Lists/Search> before posting!
Please don't post (un)subscribe requests to the list. Use the www
interface or send it to gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>.
Can't post? Read http://www.gromacs.org/__Support/Mailing_Lists
<http://www.gromacs.org/Support/Mailing_Lists>
--
========================================
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
========================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
