[gmx-users] Pdb files generated on Lincs warning

Justin Lemkul jalemkul at vt.edu
Mon Nov 27 14:33:39 CET 2017

On 11/27/17 1:04 AM, atb files wrote:
>              Dear Users,When there is a Lincs warning (sometimes because of exceeding warnangle etc) the gromacs generates pdb files. My questions is:What is purpose of generating pdb files? What information they give? Which information we need to look for to analyse those pdbs. ThanksYogi Sent using Zoho Mail

These are the coordinates before and after applying constraints for each 
domain of the system. They are not PBC-corrected so they can be really 
hard to interpret. mdrun prints which atoms are having issues, which is 
usually sufficient to begin diagnosing what is going on.



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

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

jalemkul at vt.edu | (540) 231-3129


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