Re: [gmx-users] density vs time

2010-03-16 Thread Justin A. Lemkul
nishap.pa...@utoronto.ca wrote: Near the end, the values are fluctuating around one. The reason I was That would seem right to me. trying to get density values was may be to try an understand if the density computed by gromacs is different for just water system and water+one methane sys

Re: [gmx-users] density vs time

2010-03-16 Thread nishap . patel
I am trying to get an rdf graph actually, and my values are very close to one, but not exactly one, and I was wondering if there is some normalization issue with g_rdf? These are my values for rdf: 0 0 0.002 0 0.004 0 0.006 0 0.008

RE: [gmx-users] density vs time

2010-03-16 Thread Dallas B. Warren
g_energy Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hamm

Re: [gmx-users] density vs time

2010-03-16 Thread Justin A. Lemkul
Justin A. Lemkul wrote: nishap.pa...@utoronto.ca wrote: Hello, I am simulating one methane molecule in 899 water molecues in the box size of 3 3 3 nm (27nm^3). I would like to determine density vs time. Is there a way I can do that? I am running my simulation at constant Volume i.e.

Re: [gmx-users] density vs time

2010-03-16 Thread Justin A. Lemkul
nishap.pa...@utoronto.ca wrote: Hello, I am simulating one methane molecule in 899 water molecues in the box size of 3 3 3 nm (27nm^3). I would like to determine density vs time. Is there a way I can do that? I am running my simulation at constant Volume i.e. no pressure coupling. I tri