Re: [AMBER] Thermodynamic integration goes wrong in lambda =0 while lambda = 1 is ok!!

From: David A Case <>
Date: Thu, 6 Aug 2015 12:55:44 -0400

On Thu, Aug 06, 2015, Khabiri, Morteza wrote:
> I am running thermodynamic integration with amber, pmemd on cpu,
> Amber14. I am using the following input file for running:
> TI simulation
> &cntrl
> imin = 0, nstlim = 150000, irest = 1, ntx = 5, dt = 0.002,

You are setting irest=1, but it is not clear where the intial coordinates
came from. You talk about having minimized the system with lambda=0.
Make sure that when you put those coordinates into the MD calculation (which
will mean you have to set irest=0) that the starting energy matches the
minimized energy.

> I started the restart simulation from a previous run.

This is not very clear (at least to me): what was the "previous run"? Did it
also have lambda=0? It looks (from admittedly limited evidence) that the
problem is in the coordinates created by this previous run.


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Received on Thu Aug 06 2015 - 10:00:03 PDT
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