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 ions.) 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 problems. Kind Regards -- Ozge Engin ★☆
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