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
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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