[gmx-users] g_dist and vsites

[Joe Joe]

I am looking the the gmxdump output and everything seems consistent. The
only difference is that the numbering in the index file starts at 1 whereas
in the gmxdump the arrays are indexed starting at 0. The coordinates look
just fine.

Thanks,

Ilya



On Tue, Mar 9, 2010 at 10:30 AM, Joe Joe <ilchorny at gmail.com> wrote:

> I  trjconv/ed xtc to pdb and loaded into vmd. The coordinates looked fine.
>
> I also
>
> tpbconv/ed topol.tpr to topol_subset.tpr.
>
> then I
>
> editconf/ed topol_subset.tpr to gro and looked at the coordinates. Index
> file matched and structure looked whole in vmd.
>
> I will try the gmxdump
>
> Thanks,
>
> Ilya
>
>
>
>
> On Tue, Mar 9, 2010 at 10:22 AM, David van der Spoel <spoel at xray.bmc.uu.se
> > wrote:
>
>> On 2010-03-09 19.16, Joe Joe wrote:
>>
>>> yep.
>>>
>> Have you gmxdump/ed the xtc to check the coordinates are right?
>>
>>>
>>> On Tue, Mar 9, 2010 at 10:15 AM, David van der Spoel
>>> <spoel at xray.bmc.uu.se <mailto:spoel at xray.bmc.uu.se>> wrote:
>>>
>>>    On 2010-03-09 19.09, Joe Joe wrote:
>>>
>>>        Hi I am trying to post process and xtc trajectory using g_dist. I
>>> am
>>>        trying to calculate the CA-CB distance of an Alanine residue but
>>>        I get
>>>        NAN in all the distance columns. It works for the other residues
>>>        I've
>>>        tried (i.e. SER, VAL). I am using vsites in my simulation and I
>>>        think it
>>>        may have some thing to do with the way gromacs outputs the CB
>>>        positions
>>>        in the xtc file when the CB is part of the vsite network. Any
>>>        thoughs?
>>>
>>>        Thanks,
>>>
>>>        Ilya
>>>
>>>    Are you sure your index file matches the xtc/tpr?
>>>
>>>    --
>>>    David van der Spoel, Ph.D., Professor of Biology
>>>    Dept. of Cell & Molec. Biol., Uppsala University.
>>>    Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
>>>    spoel at xray.bmc.uu.se <mailto:spoel at xray.bmc.uu.se>
>>>
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>>
>> --
>> David van der Spoel, Ph.D., Professor of Biology
>> Dept. of Cell & Molec. Biol., Uppsala University.
>> Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
>> spoel at xray.bmc.uu.se    http://folding.bmc.uu.se
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