On Thu, May 05, 2011, siddesh southekal wrote:
>
> After I minimize the system (ligand-protein complex) and then I try to run
> MD in the heating stage , the simulation runs without any problem ( but as
> long as the wall clock is given , which should end in much shorter time )
> and completes without any error in the .out file .
We need to know whether the mdout file completed normally, e.g. has timing
info at the end, and so. I suggest you try a run with nstlim=10 and ntpr=1
and look carefully to see if everything is OK. It might be worth trying both
sander and pmemd on this short run, just to see if there is any difference.
> But the .rst file is useless and
> cannot be used to restart the simulation , and has only 3-4 frames .
This doesn't make good sense: restart files only contain one time point. I
wonder if you are confusing trajectory files with restart files?
....dac
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Received on Thu May 05 2011 - 06:30:03 PDT
