[gmx-users] trjconv index mismatch

[Alex]

Yes, there are more atoms in the system, but only 2837 of them are labeled
"CNT.' Well, I could share the files with you, of course, but you're
running the latest version, aren't you? :)

On Mon, Apr 18, 2016 at 5:23 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 4/18/16 7:20 PM, Alex wrote:
>
>> Justin,
>>
>> I understand what you're saying, but for the life of me I can't understand
>> where this discrepancy is coming from, because the input coordinates have
>> 2837 CNT atoms, and trjconv selector menu lists that number correctly.
>> Completely lost here. Are there any alternatives to output (in mdp) the
>> correct group?
>>
>>
> Without access to your files, there's nothing else I can really tell you.
> Presumably there are more atoms in the system, yes?  Your index group
> somehow specifies out-of-range atoms.  Or maybe trjconv isn't parsing the
> .tpr properly (use convert-tpr to output a matching .tpr that has only CNT
> and try again).  I feel like there was an issue with this some time ago;
> 5.0.5 is considered old nowadays so the bug should have been fixed :)
>
> -Justin
>
>
> Alex
>>
>> On Mon, Apr 18, 2016 at 5:15 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>>>
>>> On 4/18/16 6:17 PM, Alex wrote:
>>>
>>> Hi all,
>>>>
>>>> I've got a system that includes a group named "CNT" consisting of 2837
>>>> atoms. To save space, I am outputting (at a very high rate) a compressed
>>>> trajectory that contains only that group. The GMX version is 5.0.5.
>>>> Here's
>>>> the relevant mdp excerpt:
>>>>
>>>>
>>>> nstxout             =  10000
>>>> nstcomm             =  1000
>>>> nstxout-compressed  =  10
>>>> compressed-x-grps   =  CNT
>>>> nstvout             =  1000
>>>> nstfout             =  500
>>>> nstlog              =  100
>>>> nstenergy           =  500
>>>> nstlist             =  20
>>>>
>>>> Upon trying to convert the compressed trajectory, after selecting the
>>>> appropriate group from the menu (CNT, 2837 atoms), I get:
>>>>
>>>> command: trjconv -f traj_comp.xtc -s prod.tpr -o test.pdb
>>>>
>>>> output:
>>>> -------------------------------------------------------
>>>> Program trjconv, VERSION 5.0.5
>>>> Source code file:
>>>> /home/smolyan/Downloads/gromacs-5.0.5/src/gromacs/gmxana/gmx_trjconv.c,
>>>> line: 1330
>>>>
>>>> Fatal error:
>>>> Index[2645] 2838 is larger than the number of atoms in the
>>>> trajectory file (2837). There is a mismatch in the contents
>>>> of your -f, -s and/or -n files.
>>>> For more information and tips for troubleshooting, please check the
>>>> GROMACS
>>>> website at http://www.gromacs.org/Documentation/Errors
>>>>
>>>> Where's this single-atom discrepancy coming from? Any suggestions?
>>>>
>>>>
>>>> Whatever you selected as output contains more atoms than are in the
>>> trajectory.  Note that it's not necessarily a single-atom discrepancy,
>>> it's
>>> just that the fatal error is triggered as soon as an index that is out of
>>> range is identified.  You're only outputting CNT, and presumably the .tpr
>>> contains more atoms, so the selection you're making can only be CNT or
>>> some
>>> subset of those atoms.
>>>
>>> -Justin
>>>
>>> --
>>> ==================================================
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>>
>>> Department of Pharmaceutical Sciences
>>> School of Pharmacy
>>> Health Sciences Facility II, Room 629
>>> University of Maryland, Baltimore
>>> 20 Penn St.
>>> Baltimore, MD 21201
>>>
>>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>>> http://mackerell.umaryland.edu/~jalemkul
>>>
>>> ==================================================
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> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
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> Gromacs Users mailing list
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