AMBER Archive (2004)

Subject: Re: AMBER: Gibbs and solvent caps

From: Miguel de Federico (
Date: Mon May 03 2004 - 05:28:47 CDT


 I had the same problem you have now. Everything was ok, with sander and when
I started gibbs simulations the temperatura rised to absurd high values and
the system blowed up. By shortening the time step (dt) the simulation was
stable for some more steps, but the final sollution that worked me OK was
using using SHAKE for all bonds. (ntc=3, ntf=3).

 You can try this, and see it its improving...


> Hi... I have been trying to run a Gibbs simulation with a solvent cap.
> I have received no error and everything worked perfectly during the
> minimization and equilibration in Sander. However, in Gibbs, as soon
> as the simulation starts, the system blows up (coordinates get out of
> range and temperature rises quickly out of range). I know the solvent
> cap is the problem since the same .top and .crd files with the cap
> inactivated in the gibbs input works fine... can anyone help me with
> that problem?
> Thanks

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