Re: AMBER: question on protein folding simulation

From: Gustavo Seabra <>
Date: Mon, 4 Dec 2006 13:31:54 -0500


If you want to keep those velocities, than yoou'll have to write a
program. Here's what I can suggest:

1. Run the calculation on your "big" system (part I). I suggest that
you use iwrap=1 to keep the coordinates wrapped inside the box.

When the time comes to reduce your system, here's where you'll have to
do some coding:

2. Save a copy of your restart file to a different file.
3. Run your old restart file through ptraj to center the protein, then
wrap all waters around it. Notice that ptraj will loose all
velocities, but you have saved them in the step above.
4. Restore the velocities from the original restart file into the new
(centered) restart file.
5. Write a program that will, based on the coordinates of your new
box, keep all molecules that are inside it. This program will:
     a. Go through your (centered) restart file,
     b. Check the coordinates of all atoms
     c. Get all residues that lie inside the new box.
     d. Write a new restart file containing only those residues
(coordinates and velocities)
6. Now that you have a new restart file, all youo need to do is to
edit the parmtop file to remove the extra waters. This step should be
simple, but others in this list should be able to give you more
detailed help on this step.

Just make sure that you keep the same file formatting when writing the
new restart and parmtop files. Also, I believe you might still need a
bit of equilibration, since the size of the system changed...


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Received on Wed Dec 06 2006 - 06:07:32 PST
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