[gmx-users] huge center of mass distance mismatch in umbrella sampling

[Justin Lemkul]

On 1/21/18 6:53 PM, Irem Altan wrote:
> Hi,
>
>
> I have two copies of a protein that are in contact with each other. Their center of mass distance is about 5.5 nm. However, in the resulting potential of mean force, there is an energetic minimum at 3.5 nm. How is this at all possible? At that distance half of the protein would be overlapping each other. How could I diagnose why this is happening?

Watch the trajectory from that window. Have the proteins reoriented? 
What was the initial COM distance, and how long was the reaction 
coordinate? What are your .mdp settings?

-Justin

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Justin A. Lemkul, Ph.D.
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Virginia Tech Department of Biochemistry

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