[gmx-users] g_dist and vsites

[Joe Joe]

I also just tried on a different ALA and got the same problem.

Ilya


On Tue, Mar 9, 2010 at 10:58 AM, Joe Joe <ilchorny at gmail.com> wrote:

> 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>
>>>>
>>>>    http://folding.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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>>
>>
>
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