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

Irem Altan irem.altan at duke.edu
Mon Jan 22 23:55:32 CET 2018

I actually noticed that in md_pull.mdp I have

pull_group1_name        = Chain_A

pull_group2_name        = Chain_B

which is the correct order as the pull simulation looks fine.

However, in md_umbrella.mdp,

pull_group1_name        = Chain_B

pull_group2_name        = Chain_A

which is wrong. However, since pull rate is 0 in the actual umbrella sampling simulation, why would this affect the center of mass distance? How does Gromacs measure the center of mass distance to write to the pullx file? When I check the distance with gmx distance, I get the correct value of 5.5 nm. But the pullx files have the wrong values: 3.5 nm.

In this case can I get away with manually creating pullx files from the trajectories themselves?



From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Justin Lemkul <jalemkul at vt.edu>
Sent: Monday, January 22, 2018 7:50:29 AM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] huge center of mass distance mismatch in umbrella sampling

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 A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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