[gmx-users] Problems with umbrella sampling

Berk Hess gmx3 at hotmail.com
Fri Mar 12 08:46:29 CET 2010


I think you want pull_dim = Y Y Y
and for umbrella sampling you need pull=umbrella


Date: Thu, 11 Mar 2010 17:37:34 -0800
From: jrcasey20 at gmail.com
To: gmx-users at gromacs.org
Subject: [gmx-users] Problems with umbrella sampling


I am interested in creating a PMF for Na+ and I- in the presence of THF (tetrahydrofuran).  I am having a couple of issues though.

First, I have followed the umbrella sampling tutorial on the gromacs website very careful, and I think I am doing everything right.  I minimized the energy of my system, did a short equilibrium run, and then pulled Na+ and I- away from each other at a specified rate.  This generated starting configurations, which I used in my umbrella sampling (see attached file ).  Once I had many umbrella sampling windows, I used g_wham to recombine them.  First I looked at the histograms.  I have good overlap, but I notice some very odd features:

1)  I see substantial shifting towards lower distances between Na+ and I-, no matter what the initial distances they start separated at.  I would expect this if I am near an equilibrium distance, but I see it for all distances.

2)  My original pull simulation (where I specificed a rate) started Na+ and I- 0.27 nm apart.  All of my starting configurations are 0.27 nm apart or further.  If I run some of the umbrella sampling simulations at 0.27 nm, I see that the Na+ and I- reach distances as low as 0.03 nm!  This is completely unphysical (both in that my spring constant is strong enough to supposedly prevent such large drifts and because the two molecules should not want to be on top of each other).  

To check these issues out, I tried to do a couple of things:

I want to pull the Na+ and I- closer together than 0.27 nm, and see if I get the steep increase in energy, like I expect.  I am having problems with this part though.  I have not been able to pull my molecules closer together when starting at 0.27 nm, so I tried to start them closer together and then pull them apart by using the following in my .mdp file:

pull = constraint
pull_geometry = distance
pull_dim = Y N N
pull_start = yes
pull_ngroups = 1
pull_group0 = Na+
pull_group1 = I-
pull_vec1 = 1 0 0
pull_init1 = 0.1 (I think this means that I- starts 0.1 nm away from Na+?)

pull_rate1 = 0.005

When I do this, I still get my molecules being pulled apart from 0.27 nm to further distances apart.  I also tried using no pull_init1, but using pull_vec1 = -1 0 0, but that didn't work either.  Whenever I tried to use pull_geometry = position, I got segmentation faults...

Has anyone else experienced these issues?  Is there a way to bring Na+ and I- closer?  I have checked older posts, but the suggestions I keep seeing (i.e. use pull_init1) aren't working for me.

Thank you!

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