[gmx-users] g_dist and vsites

[Joe Joe]

done, bug #402

On Tue, Mar 9, 2010 at 11:44 AM, David van der Spoel
<spoel at xray.bmc.uu.se>wrote:

> On 2010-03-09 20.01, Joe Joe wrote:
>
>> I also just tried on a different ALA and got the same problem.
>>
>
> can you please submit a bugzilla and upload files to reproduce the problem?
>
>
>> Ilya
>>
>>
>> On Tue, Mar 9, 2010 at 10:58 AM, Joe Joe <ilchorny at gmail.com
>> <mailto: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
>>    <mailto: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 <mailto: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>
>>                <mailto: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>
>>                <mailto: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 <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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