[gmx-users] trjconv index mismatch

[Alex]

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?

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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