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
#ifdef POSRES_WATER
; 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
--
========================================
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
========================================
--
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
