Box info after minimization

From: Troy Bothwell <>
Date: Wed 4 Apr 2001 22:38:58 -0500

Hello all,

I am confused about how to assure the correct periodic box conditions when
restarting a run after minimization. If I do constant pressure md, then
minimization, followed by md again the web site says:

One very important point to note is that you want the box coordinates
specified here to match the inpcrd or restart from the previous run. The
prmtop file is not updated as the run progresses with the current box
information. However, box size changes during constant pressure runs. Box
information is only read into sander from the inpcrd file directly when NTX
= 7 (i.e. read velocity and box information). Post minimization, no box
information is written. Therefore, if you do dynamics, followed by
minimization, followed by dynamics with PME, you need to update the mdin
file with the box size from the previous dynamics steps. This information is
contained in the final line of the restart file.

However I seem to remember a rather lengthy discussion on the reflector (I
can't seem to find the messages in the archive) about which box information
takes precedence (i.e. restart file overrides the parmtop box info).

I am using amber6 and need to be clear on the correct way to assure the box
information is correct in this situation. Is the procedure on the website
the best route in amber6?


Received on Wed Apr 04 2001 - 20:38:58 PDT
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