Dear Wang,
You could use ptraj to shrink your mdcrd file by removing frames. E.g.
trajin foo.mdcrd 1 100000 100
trajout foo2.mdcrd
This would give you frames 1, 101, 201 etc up to 999901 thus shrinking your mdcrd file 100 fold. In your case this would be equivalent to ntwx=10000.
All the best
Ross
> -----Original Message-----
> From: amber-bounces.ambermd.org [mailto:amber-bounces.ambermd.org] On
> Behalf Of Yunfen Wang
> Sent: Wednesday, May 05, 2010 7:20 AM
> To: amber
> Subject: [AMBER] ntpr ntwx too small
>
> Hi all,
> During my MD process, I have set a bit small number for ntpr,
> that is, ntpr = 100, ntwx = 100
> besides, my step is low , 0.5fs . So , my output is too large to
> analyse . In fact , that every 1000 steps the coordinates is written
> to file "mdcrd" is ok .
> So, anyone has suggestions dealing with it except for running the MD
> process oncemore .
> Thanks a lot!
> wang
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Received on Wed May 05 2010 - 08:00:04 PDT
