Thank you Jason.
When I was not using iwrap=1, after ~ 60 ns or so I was getting
coordinates overflow warning. Now I will try to use ioutfm=1 and ntxo=2
for my new simulations. Hoping it won't give any problem. If we get such
problem again can we change it back to iwrap=1?
Sunita
> On Mon, 2014-09-08 at 18:02 +0530, sunita.tifrh.res.in wrote:
>> Dear Prof. Case,
>>
>> You have specified ntxo=2, but in the Amber12 manual ntxo= 0
>> (Unformatted
>> (no longer recommended or allowed: please use formatted restart
>> files)
>> OR
>> =1 (default) Formatted (ASCII) are there.
>>
>> I didn't find an option ntxo=2.
>>
>> Is there such option ??
>
> Yes. See the errata for the manual at http://ambermd.org/doc12/
>
>> I have also a question on iwrap. If we set ioutfm=1 then we don't have
>> to
>> set iwrap=1 even for long simulation. Am I write ?
>
> If you set ioutfm=1 and ntxo=2, then you will never see the problem that
> coordinates overflow fixed-size fields and replaces the coordinates with
> ***s. It's possible to run long enough that the single-precision
> trajectory files may lose precision for the particles that have migrated
> very far away from the original box, though (although you probably have
> to run for a very long time for this to become a real problem).
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
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Received on Mon Sep 08 2014 - 06:30:04 PDT
