From: Alberto p <>
Date: Wed, 29 Dec 2004 13:07:48 +0100 (CET)

Hi everyone,
I have some doubts about nscm and the results in simulations. I started some DNA in explicit solvent simulations a while back using amber6. For these simulations I used the keyword NTCM = 1 which removes the CM translation at the beggining of the simulation (I'm restarting every 100 ps so I guess that's when sander removes CM translation). NSCM was left at its default value of 0.
Now I'm trying to continue the simulations with amber8. First I ran 800 ps of simulation to compare with my results of amber6. I left the defaults for NSCM as they were,NSCM = 1000. When analyzing the total energy I see that is rises some 200 kcal from where the simulation was running with amber6 and then stabilizes. Checking the difference in keywords I noticed that when putting NSCM = 999999 the energies amber8 and amber6 were the same.
Looking at the rms the structures seem to be more or less the same, and once the energies are stabilized (which happens really quickly) no anomalities are seen.
So my question is twofold:
i.) Would it be wise to continue the simulation removing the CM translation every 100 ps?
ii.) How does sander do the recalculation of velocities? Does it remove the COM velocity and then rescale according to the temperature or does it do something different?
I've no one around to ask for help on the subject, so any hint would be gratly appreciated,
thanks in advance

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Received on Wed Dec 29 2004 - 12:53:00 PST
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