Dear tec3
> Note that with either the closest or this option, you will still
potentially have artifacts from the "holes" left over from the missing
peptides which will be problematic if there is close peptide-peptide
association...
Yes. It is much better if I could cluster molecules *without* removing
them and have complete trajectories of each clusters (I don't care if it
is duplicated or not).
That's why I asked this but it sounds not possible...
> Note also, that investigating "dynamics" of water around a cluster is
not defined since there would no longer necessarilly be equal time
between frames
I said 'dynamics' but actually it is not so sequential data is not
required. But anyway thanks for your note :-)
Regards
Asai
On 2015年01月31日 00:36, Thomas Cheatham wrote:
>> Aha! I think I got it.
>> 'closest' command modify coordinate frame *and topology* (not like
>> 'strip') so write out the modified topology with 'parmwrite' and use the
>> modified topologies to load the produced trajectories right?
> ...while this will generate smaller trajectories, it will be rather
> computationally demanding to generate... A simpler approach if you have
> ample disk space is to simply strip out all the peptides except one, for
> each peptide, keeping the water and ions. Note that with either the
> closest or this option, you will still potentially have artifacts from the
> "holes" left over from the missing peptides which will be problematic if
> there is close peptide-peptide association... [Note also, that
> investigating "dynamics" of water around a cluster is not defined since
> there would no longer necessarilly be equal time between frames.]
>
> --tec3
>
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Received on Fri Jan 30 2015 - 08:00:06 PST
