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