I'm forwarding this to Qin who is in charge of force computation in pbsa ...
Ray
---------- Forwarded message ----------
From: Dr. Holger Kruse <kruse.ceitec.muni.cz>
Date: Mon, Dec 3, 2012 at 9:08 AM
Subject: [AMBER] pbsa forces printout from sander (amber12)
To: amber.ambermd.org
Hi everyone,
I want to combine sander (amder12) with an external (self-written)
optimizer. For gbsa computations it works as expected and
I get basically the same result as the optimization with sander itself.
However, for pbsa computations my approach does not work.
(see below for inputs)
For gbsa I generate the file "forcedump.dat", from which I read the "Total
Forces" section to get the gradient.
For pbsa, reading simply the "forcedump.dat" file leads to a very chaotic
optimization behavior.
It seems the gradient is incomplete.
I know I can generate a "force.dat" file from the &pb section
with frcopt=2, but I dont know if I need it.
Sander also computes the forces 4 times with my input ("qE forces" are to
be found 4 times in force.dat)
Any suggestions or hints?
Cheers,
Holger
--------gbsa input
&cntrl
imin=1, ntmin=1, ntx=1, ntpr=10,
maxcyc=1, ncyc=1, igb=1, ntf=1, ntc=1,
ntb=0, irest=0
/
&debugf
do_debugf=1,dumpfrc=1
/
&end
---------
--------------pbsa input
Minimization PB calculation
&cntrl
imin=1, ntmin=1, ntx=1, ntpr=1,
maxcyc=1, ncyc=1, igb=10, ntf=1, ntc=1,
ntb=0, irest=0
/
&pb
npbverb=0, istrng=0, epsout=80.0,
epsin=1.0, sprob=1.6, radiopt=1,
space=0.5, nbuffer=0, accept=0.001,
cutnb=0, dbfopt=1, npopt=2,
maxitn=100,frcopt=2
/
&debugf
do_debugf=1,dumpfrc=1
/
&end
--------------
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Received on Mon Dec 03 2012 - 10:00:02 PST
