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

fatemeh ramezani fr_750 at yahoo.com
Sat Jan 19 16:46:07 CET 2013

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?

many thanks

Fatemeh Ramezani

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