Hi Niel,
thanks a lot for your help, however, I still have some problems
with the corrected sff2.c file. The job ends but the structure is
not optimized and the thresholds are not reached.
---
[...]
ff: 1150 -181.57 139.47 -11.70 -309.34 0.00 0.00 2.15e-01
ff: 1200 -181.79 139.28 -11.43 -309.65 0.00 0.00 1.49e-01
ff: 1250 -181.93 139.15 -11.46 -309.62 0.00 0.00 1.33e-01
conjgrad returns 6791168
mm_options: ntpr=1
ff: 1 -182.00 139.08 -11.56 -309.52 0.00 0.00 9.28e-02
iter Total bad vdW elect nonpolar genBorn frms
ff: 1 -182.00 139.08 -11.56 -309.52 0.00 0.00 9.28e-02
adding 0.00000 to diagonal of the hessian
rms of search direction: 0.0928448
For alpha = 0.00000 energy = -181.9997535222
For alpha = 1.00000 energy = 2707.8188260277
For alpha = 0.00085 energy = -182.0018521355
For alpha = 0.00085 energy = -182.0018521178
newton returns 2629632
iter Total bad vdW elect nonpolar genBorn frms
ff: 1 -182.00 139.08 -11.56 -309.53 0.00 0.00 8.98e-02
RMS gradient = 8.98052e-02
dysev time = 0.42 seconds
- Thermochemistry - [...]
---
where I have in the .nab file
---
//conjugate gradient minimization
ier = conjgrad(x, 3*m.natoms, fret, mme, 0.1, 0.001, 4000);
printf( "conjgrad returns %d\n", ier );
//Newton-Raphson minimization
mm_options( "ntpr=1" );
ier = newton( x, 3*m.natoms, fret, mme, mme2, 0.0000001, 0.0, 0 );
printf( "newton returns %d\n", ier );
---
this happens with or without the use of the bsc0 parameters.
did it work in your case?
thanks a lot
sincerely
claudio
________________________________________
From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf Of NIEL MICHAEL HENRIKSEN
Sent: Friday, August 08, 2008 8:50 AM
To: amber.scripps.edu
Subject: RE: AMBER: NAB conjgrad returns error?
Subject: RE: AMBER: NAB conjgrad returns error?
Hey Claudio,
> run.x: sff2.c:1349: ephi2: Assertion `fabs(3.14159 - Phase[atyp]) < 0.01' failed.
I have been trouble-shooting the exact same problem. The problem appears to be related to the bsc0 parameters used to build the prmtop file. bsc0 allows for non-integer*pi values for the DIHEDRAL PHASE in the prmtop. You'll find if you make the prmtop using an older force field (i used ff99SB) you won't get the error. I suspect there will have to be some tweaks to the code to resolve this issue.
best,
Niel
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Received on Wed Aug 13 2008 - 06:07:29 PDT