[gmx-users] bug in trjconv?

Justin Lemkul jalemkul at vt.edu
Wed Apr 11 13:29:19 CEST 2018

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 A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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