[gmx-users] au-protein simulation, water constraint_algorithm
jalemkul at vt.edu
Sat Jan 19 16:47:52 CET 2013
On 1/19/13 10:46 AM, fatemeh ramezani wrote:
> Dr. Justin
> In GOLP paper is written: Water molecules were kept rigid with the SETTLE algorithm,
> but in its commented md.mdp file is written
> define =
> ;GOLP has been tested with lincs only
> constraint = none
> constraint_algorithm = lincs
> according to manual, SETTLE can be selected in the topology, means that with the above settings in md.mdp file, should I add
> [ settles ]
> ; OW funct doh dhh
> 1 1 0.1 0.16333
> in .top file?
> Are these settings correct?
> If that is the constraint = none, constraint_algorithm = lincs applies?
The SETTLE algorithm is always used for water unless -DFLEXIBLE is defined in
the .mdp file. Note the #ifdef blocks in the topology for water.
Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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