[gmx-users] g_dist and vsites
Joe Joe
ilchorny at gmail.com
Wed Mar 10 18:42:56 CET 2010
I think I know the problem. I looked through gmx_dist and the distance is
calculated using the center of mass of the group. Since I am using Vsite the
mass of CB in ALA is set to zero. Is that correct?
Thanks,
Ilya
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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