[gmx-users] Are water molecules restrained "by default"?
addiw7 at googlemail.com
Mon Jul 27 23:18:29 CEST 2015
Dear Gromacs Experts,
I read in Gromacs documentation that
will be interpreted to restrain position of all water oxygen atoms. However
if I understand it correctly I should define where proper *itp file is
present as it is for restraining heavy atoms of my protein molecule:
; Include Position restraint file
I neither use #include mechanism for water oxygens nor #define.
However I do not get any errors as the documentation suggest when
POSRES_WATER is not defined.
So my question is whether using this what grompp has generated regarding
restraining water oxygens:
; Position restraint for each water oxygen
[ position_restraints ]
; i funct fcx fcy fcz
1 1 1000 1000 1000
is enough to actually restrain those atoms? Or my atoms are not restrained
However if they are, how does Gromacs know what atoms are water oxygen
atoms? Simply it "recognizes" them because POSRES_WATER flag is used and
somewhere in my *top file I include *itp file for water molecues:
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