I am sorry. It was typo. It should be "prof" instead og "prog".
On Sun, Sep 7, 2014 at 7:33 AM, Setyanto Md <stwahyudi.md.gmail.com> wrote:
> Dear Prog. Case
>
> thank you for your answer.
>
>
> On Thu, Sep 4, 2014 at 7:01 PM, David A Case <case.biomaps.rutgers.edu>
> wrote:
>
>> On Thu, Sep 04, 2014, Setyanto Md wrote:
>> >
>> > I read at the amber 12 manual book on page 20, in the section of iwrap.
>> > It is mention "..For very long runs, setting iwrap = 1 may be required
>> to
>> > keep the coordinate output from overflowing the trajectory and restart
>> file
>> > formats,..."
>> >
>> > How long of the simulation can be count as very long simulation ?
>>
>> There is no general answer to this question: it depends a lot on the
>> nature of
>> the solute and the size of the simulation box.
>>
>> > For iwrap=0, can we make it wrap again after simulation, maybe with some
>> > process ?
>>
>> The cpptraj program can "unwrap" trajectories that have been wrapped.
>> Another
>> useful strategy is to set ntxo=2 (using the netcdf restart format), which
>> does
>> not have the problem of overflowing a fixed field length.
>>
>> ....dac
>>
>>
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>
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Received on Sat Sep 06 2014 - 18:00:03 PDT
