Hi Holger,
I used your input pasted here and was able to get forcedump.dat for both pb and gb and they are in the same format.
The "Total Forces" sections gives the force on every atom. The numbers are different but still consistent between pb and gb.
So, to better understand what your problem is, could you email us your topology and coordinate files as well as your output files? See if we can reproduce.
All the best,
Qin
On Dec 3, 2012, at 11:53 AM, Ray Luo, Ph.D. wrote:
> 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 - 15:30:02 PST
