[gmx-users] ffgmx:diffusion of oxygen

Dallas B. Warren Dallas.Warren at pharm.monash.edu.au
Wed Apr 29 00:46:33 CEST 2009

The issue is you don't have enough statistics to get a meaningful
result.  Three ways you can get more, more particles, more time, or
multiply runs.

Catch ya,

Dr. Dallas Warren
Department of Pharmaceutical Biology and Pharmacology
Pharmacy and Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at pharm.monash.edu.au
+61 3 9903 9167
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 Sunil Thapa
	Sent: Tuesday, 28 April 2009 5:40 PM
	To: gmx-users at gromacs.org
	Subject: [gmx-users] ffgmx:diffusion of oxygen
Respectable Experts
Thank you very much David. Yes the msd curve tries to improve if I run
for 100ns. But my system is very small 1oxygen molecule in 255 molecules
of water. I want to calculate the self diffusion coefficient of oxygen .
What I have found that people do such simulations for mostly not more
than 10 ns. I also got to see your paper on dynamic property of
water/alcohol mixture where you have used time less than 10 ns. Which
msd curve is to take ?
Another query : I want to simulate the system in a bit higher
temperature 310 K . What are the parameters I should change in the mdp
file. I saw the previous mails about it. Eric says that only time step
should be small in order to constrain the bonds. Are there any other

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