Some question about Target MD

From: Yang Gao (yanggao_at_iastate.edu)
Date: Tue Aug 05 2008 - 10:40:10 CDT

Dear all,

I am learning now how to use Target MD to do some simulation work and have
something uncertain about it, hope some of you could give me some suggestions:

First, should it be run in a vacuum environment? as it says, there should be
equal number of atoms in the starting structure and the target structure. But in
my structure files, there is big difference in number of water and they present
in different position. I do not know how to equal them. And could i add a water
box or something with equal number of water?

Second, can i arrive the final structure with a smaller TMDk. I have tried
different TMDk and time step. As i observe in my case, if i set up TMDk, 200 (i
have tried 0.1, 0.2, 0.5, 1, 2, 5ns), the run stop at around rmsd~4. Even I
restart a new run from there, the rmsd didnot seems decrease much. Is that mean
there may be some energy barriers there and with the current TMDk, i can not
pass it?

Third, can it arrive the target structure with a rmsd 0. I have tried set up
very high TMDk (10000, 20000), and the final rmsd is less than 1. But i wonder
if it is possible to arrive 0.

Thank you very much.

 Yang

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