Re: [AMBER] Amber:SANDER BOMB:volume of ucell too big, too many subcells

From: David A Case <>
Date: Wed, 21 Dec 2011 08:33:04 -0500

On Wed, Dec 21, 2011, shradhey gupta wrote:
> i am facing problem to run md simulation of pure methanol of 367 molecules

> i observed that volume of box
> is becoming bigger and bigger with simulation run time as well as decrease
> in density.

This is the origin of the problem. Restarting sander (or better, using
pmemd if possible) should allow the simulation to continue. But you may
have a force field problem: the boiling point of (real) methanol at 1
atm. is 338K, are you are not far below that. Depending on how you came
up with parameters, the methanol in your force field might not have enough
cohesive energy to remain a liquid at these conditions-- your density is way
below that of liquid methanol.


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Received on Wed Dec 21 2011 - 06:00:04 PST
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