[gmx-users] trjconv index mismatch

[Justin Lemkul]

On 4/18/16 7:27 PM, Alex wrote:
> 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? :)
>

As you might expect, yes.

Do the atom numbers of the CNT start from 1, or is there something else listed 
before it in the coordinates and topology?  If that's the case, making a 
matching .tpr via convert-tpr is the only option.

-Justin

> 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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-- 
==================================================

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

==================================================