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

    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

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129


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