Re: [gmx-users] bug in trjconv?

[Harry Mark Greenblatt]

BS”D

Dear Mark,


did the .tpr actually match the trajectory file?


Sorry, that was indeed the problem (mismatch of -f and -s files).

Thanks for the hint

Harry





Harry M. Greenblatt
Associate Staff Scientist
Dept of Structural Biology   
harry.greenbl...@weizmann.ac.il
Weizmann Institute of SciencePhone:  972-8-934-6340
234 Herzl St.Facsimile:   972-8-934-3361
Rehovot, 7610001
Israel

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Re: [gmx-users] bug in trjconv?

[Mark Abraham]

Hi,

It's hard to say whether there's a bug, given this information. What
version of GROMACS was it, were there any warnings on the terminal output,
did the .tpr actually match the trajectory file?

Mark

On Wed, Apr 11, 2018 at 1:14 PM Harry Mark Greenblatt <
harry.greenbl...@weizmann.ac.il> wrote:

> BS”D
>
>In a given system with several chains, after minimisation the chains
> are split up by PBC.   Using trjconv on this file to put all the chains
> back into a unified complex, the Ions are converted to water molecules.
> The input file (-f) and the reference file (-s) had waters and Ions
> (sodium and chloride), but the output file has only waters (waters have
> replaced the ions).   Seems to be a bug.
>
> Thanks
>
> Harry
>
>
>
> 
> Harry M. Greenblatt
> Associate Staff Scientist
> Dept of Structural Biology   harry.greenbl...@weizmann.ac.il
> 
> Weizmann Institute of SciencePhone:  972-8-934-6340
> 234 Herzl St
> .
>   Facsimile:   972-8-934-3361
> Rehovot, 7610001
> Israel
>
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Re: [gmx-users] bug in trjconv?

[Justin Lemkul]

On 4/11/18 7:13 AM, Harry Mark Greenblatt wrote:

BS”D

In a given system with several chains, after minimisation the chains are 
split up by PBC.   Using trjconv on this file to put all the chains back into a 
unified complex, the Ions are converted to water molecules.
The input file (-f) and the reference file (-s) had waters and Ions (sodium and 
chloride), but the output file has only waters (waters have replaced the ions). 
  Seems to be a bug.


That seems wildly unlikely, but there's no way to know unless you can 
provide actual details: GROMACS version? input files? exact command used?


-Justin

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==

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Virginia Tech Department of Biochemistry

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