[gmx-users] au-protein simulation, water constraint_algorithm

[Justin Lemkul]

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

-- 
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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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