[gmx-users] Doubt regarding popc simulations
chris.neale at utoronto.ca
Thu Jul 24 20:59:19 CEST 2008
Unless your membrane is extraordinarily large, your cutoffs extraordinarily long, or your computational resources extraordinarily small, then I suggest that you simulate for 50ns and then analyze the convergence of these properties yourself. I have often posted the 50 ns suggestion to this list, but there really is no substitute for checking statistical convergence directly and trying to make some kind of logical argument about systematic convergence.
-- but you can always do analysis on your 5ns at the same time that you run more :)
-- original message --
I want to ask one question regarding time of POPC simulations, this may be trivial query to you that is how long time normally popc alone simulations have to run? I know that if potential energy plot shows values from high to low which depicts stable graph we can stop the simulation and start doing analysis. If consider the Tieleman POPC molecule it will come energy stable from 1.5ns to final time you run.
In my case the potential energy has got stabilsed from 1.5ns so I have simulated till 5ns and stopped the POPC simulation so can I start further analysis like area per lipid, density of bilyer etc ? or I have to run some more time then I have to start membrane analysis?
Could anyone suggest me please.
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