Re: [AMBER] restart an SMD run

From: Jason Swails <jason.swails.gmail.com>
Date: Tue, 12 May 2015 08:15:29 -0400

On Tue, May 12, 2015 at 8:07 AM, Asmita Gupta <asmita4des.gmail.com> wrote:

> Thanks again,
>
>
> One last thing..i used this value as r2 and force values seems to be
> continuous now....like this:-
>
> -------------------------------------
> head dist_vs_t_2nd_run-
>
> 50.65900 49.62175 6.22351 0.00000
> 50.65901 49.63891 6.12062 0.00007
> 50.65902 49.65702 6.01198 0.00013
> 50.65903 49.67611 5.89754 0.00019
> 50.65904 49.69581 5.77938 0.00025
> ------------------------------------
>
> Shouldn't the 4th column be continuous too (values should start from
> 41.something)??
>

‚ÄčThat column is a running sum. The restart file does not contain that
information, so sander and pmemd don't know how to "continue" the work
profile. So the answer to your question is "yes, the 4th column should be
continuous", but you have to make it that way (because as you've noticed,
sander does not make it easy to restart SMD simulations).

HTH,
Jason

-- 
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue May 12 2015 - 05:30:05 PDT
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