[gmx-users] Re: About Usage of restraint
jalemkul at vt.edu
Fri Feb 8 14:50:05 CET 2013
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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
> I Have Followed the Following gromacs Hyper link to add vertical z axis Restraint
> 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.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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