[gmx-users] g_clustsize

[Mark Abraham]

Hi,

I don't understand how you can have a problem with one cluster, when the
size of that cluster is constant, but the identities of the members of the
cluster is not constant.

There may be a bug in gmx clustsize, which you might fix or hack around. If
not, I guess you have to find a way to have more than one cluster produced.

Mark

On Mon, May 25, 2015 at 6:45 PM pratibha kapoor <kapoorpratibha7 at gmail.com>
wrote:

> I would like to enlist the chain ids (A,B,C...) , of all those which are in
> cluster at each time frame.
>
> Thanks in advance
>
> On Mon, May 25, 2015 at 7:43 PM, pratibha kapoor <
> kapoorpratibha7 at gmail.com>
> wrote:
>
> > Thanks Mark for your reply.
> > I would like to extract chain ids of all the members of the maximum
> > populated cluster at each point of time. Thus, I have created a script
> that
> > would run g_clustsize at each time frame which is giving me error:
> > Fatal error:
> > Lo: 0.000000, Mid: 16.000000, Hi: 16.000000
> > This is understandable since there is only one cluster of constant size
> at
> > any particular time.
> > Due to this error, maxclust.ndx file is not created (through which I can
> > work backwards and extract chain ids).
> > Can you guide me in proceeding further?
> >
> >
> > On Tue, May 19, 2015 at 9:37 PM, pratibha kapoor <
> > kapoorpratibha7 at gmail.com> wrote:
> >
> >> Hi,
> >>
> >> I have used g_clustsize to count the number of molecules (they differ by
> >> chain id) in the maximum populated cluster. Is it also possible to label
> >> these molecules? i.e. to print chain ids of these molecules with time in
> >> separate file?
> >>
> >> Thanks in advance
> >>
> >
> >
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