[gmx-users] problem with the energy minimization of a system composed of two NA+ ions and explicit water

Ozge Engin ozge.engin at gmail.com
Tue Mar 30 13:09:53 CEST 2010

Hi all,

First of all, thank you for your quick reply Justin. Here, I want to state
the problem in a clearer way.

I have been trying to calculate the PMF between two NA+ ions in explicit
water. In order to do that I first pulled one of the NA+ ions continuously
with respect to the other until the farthest point on the PMF curve was
reached. After that I split the continuous pulling trajectory from the
points that are in correspondence with the constraint points of the PMF
curve. These were done via *genera_start_4* script.

I took each starting conformation, that was obtained from continuous
pulling, solvated with water, and then energy minimized. Then, I prepared
the systems for constraint pulling MD production runs. These were done via *
input* script. Interestingly, systems (ion+water) at some of the constraint
points could not been energy minimized, it reached to the machine epsilon,
but not to the desired criteria. The force per atom was too high, around the
order of ^4. Moreover, this issue was not distance-dependent, which means
that the energy minimization worked for smaller constraint points, but not
for some of the larger constraint points. When I looked at the problematic
trajectories, I saw that bonds of a water molecule near the box boundary was
longer. I thought that this may be due to genbox command. Because of the
small radius of NA+ ion it may not check the overlaps among the atoms. In
order to test whether it is the case I increased the LJ parameters of the
ion. This worked for some of the points, but not for others. (Note that the
diameter is still smaller than the constraint distance between the two

I use ffG45a3 force field, and the scripts given above. I tried this with
different versions of Gromacs: 4.0.7, 4.0.5, and faced with similar

Kind Regards
Ozge Engin
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