[gmx-users] bond constraints

Justin A. Lemkul jalemkul at vt.edu
Mon Aug 15 18:48:57 CEST 2011

Gavin Melaugh wrote:
> Hi all
> Sorry forgot to give a subject in the first e-mail. A very quick
> question. If I want to constrain all bonds in my system,
> is it just a case of setting  constraints = all-bonds. Do I have to
> select the constraint algorithm. Here is my mdp file, I got no errors
> but its seems that this might be too simple. Note there is no relevance
> in the name umbrella here.

You didn't attach the file, but I don't suspect it's relevant anyway.  The 
default algorithm is LINCS.  Check mdout.mdp to confirm.  In the manual, for 
keywords with enumerated values, the first one listed is the default, so if no 
explicit selection is made, the default is used.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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