Hi all,
My last post didn't receive any replies, so I'll try to rephrase.
I'm doing pbsa calculations using sander with the imin=5
trajectory reading capability. I've found that the "EPB" value
is dependent on order in which the frames of the trajectory
are read.
For instance, take a trajectory with two frames, A and B:
EPB = -12567.2929 for frame A if the order is A --> B
EPB = -12567.5574 for frame A if the order is B --> A
I believe the grid is only being calculated for the first frame.
This can actually cause sander to crash if the conformation
of the system changes drastically from one frame to the next.
This is either a bug, or there is some setting to make the grid
recalculate each step that I'm not aware of. Either way it should
be of interest to the developers of MMPBSA (hopefully).
The files to reproduce the problem are here:
http://www.amber.utah.edu/biodata/sander-pb-order/
the commands I used are:
sander -O -i sander.in -p com.topo -c inpcrds -y frames_A-B.traj -o frames_A-B.out
sander -O -i sander.in -p com.topo -c inpcrds -y frames_B-A.traj -o frames_B-A.out
I'll try to track down the problem/solution, but I'm sure there is
someone who is more familiar with the code who can do it
faster.
Thanks for any help,
--Niel
PS
my previous post:
http://archive.ambermd.org/201110/0294.html
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Received on Mon Oct 17 2011 - 20:30:04 PDT
