[gmx-users] DPOSRES not working
jalemkul at vt.edu
Thu Sep 7 14:28:43 CEST 2017
On 9/7/17 5:28 AM, Sergio Manzetti wrote:
> Hi Johannes, yes, they are there in both cases:
> ; Include Position restraint file
> #ifdef POSRES
> #include "posre_DNA_chain_E.itp"
Do you have a position restraint energy term written in your .log file,
and if so, what is its magnitude? Does your DNA start at the middle of
the box (GROMACS convention) or at the coordinate origin (like other
software)? If you watch the trajectory evolve, what happens? Does the
DNA move a lot or does it just bounce back and forth around its original
position (suggesting your box is simply too small and any time an atom
crosses a boundary, you get a jump)?
Justin A. Lemkul, Ph.D.
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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