[gmx-users] gromacs.org_gmx-users Digest, Vol 131, Issue 31

[Jernej Zidar]

Hi Justin,
  Thank you for the explanation.

Best,
Jernej

On Fri, Mar 6, 2015 at 11:01 PM,
<gromacs.org_gmx-users-request at maillist.sys.kth.se> wrote:
>> Hi there,
>>    I have a receptor with a docked ligand. I would like to perform an
>> umbrella sampling simulation to get some insights into the
>> thermodynamics of the binding.
>>
>>    Following the Umbrella Sampling tutorial I performed the 500 ps
>> pulling simulation. A visual examination of the trajectory revealed
>> there's an expected change in the position of the ligand that is
>> coincidental with a worryingly big increase in the force exerted on
>> the ligand. Link to a figure:
>> https://www.dropbox.com/s/fj3daaagimuynni/rec-lig-pos-for.pdf?dl=0
>>
>>    Is this an expected behaviour or should I try to somehow adjust the
>> direction of the pulling? If so, could you advise on a strategy to do
>> so?
>>
>
> This is expected.  You're pulling on a spring at constant velocity, so the force
> on the spring increases with increasing displacement.  It is being resisted by
> the interactions between the pulled group and the reference group.  So the
> applied force is trying to overcome restoring forces in the system.  At some
> point, they break, the pulled group has a net displacement, and the force on the
> spring drops off.