[gmx-users] Force constant for umbrella sampling potential

[dtmirij]

Farzad,
The force constant is up to you to define in the .ppa file you create for
umbrella sampling.

I ask the question about the 0.5 term because I am using Grossfield¹s WHAM
algorithm and it assumes that the biasing potential used has a 0.5 in front,
but I know for example CHARMM does not include the 0.5 and I just need to
know if this is also the case with gromacs.
Thank you.
-Dina


On 12/17/07 12:34 AM, "Farzad Molani" <farzad_c81 at yahoo.com> wrote:

> Hi dear
> I think it has got 0.5 in equation.
> U=0.5*K(r-b)2
> but I dont knoe how do I get K please help me
> 
> dtmirij <dtmirij at sandia.gov> wrote:
>>  Hello everyone,
>> 
>> I would like to know does the harmonic biasing potential for running
>> umbrella sampling in gromacs have a 0.5 in front or is the 0.5 term
>> incorporated into the force constant value that we specify?
>> On other words is the potential V=0.5*k(x-xo)^2 or V=k(x-xo)^2.
>> 
>> Thank you in advance.
>> -Dina
>> 
>> 
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