[gmx-users] Re: About Usage of restraint

Justin Lemkul jalemkul at vt.edu
Fri Feb 8 14:50:05 CET 2013

Please post all Gromacs-related questions to gmx-users.

On 2/8/13 8:46 AM, vidhya sankar wrote:
> Dear Justin Thank you for your previous Mail Reply
>                                                                 As you
> Instructed me in the Previous Mail  to insert Vertical Restraint
> I Have increased  Value of  fcz to 100000
> While  Should I make  value of fcx and fcy to Zero  ? otherwise may  i Leave it
> as such
> ; Position restraint for each water oxygen
> [ position_restraints ]
> ;  i funct       fcx        fcy        fcz
>     1    1        1000      1000     1000000
> #endif
> I Have Followed the Following  gromacs Hyper link to add vertical z axis Restraint
> http://www.gromacs.org/Documentation/How-tos/Position_Restraints
> Is My way is correct or Wrong?

Wrong.  What I suggested was a restraint along z only, allowing the water 
molecules to move within the x-y plane but not descend into the hydrophobic core 
of the membrane.  The force constant in x and y should be zero, the value in z 
can be whatever you choose, but the default value of 1000 should be fine.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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