AMBER Archive (2008)

Subject: RE: AMBER: NAB conjgrad returns error?

From: Carra, Claudio (JSC-SK)[USRA] (claudio.carra-1_at_nasa.gov)
Date: Mon Aug 11 2008 - 16:14:12 CDT

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_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of NIEL MICHAEL HENRIKSEN
Sent: Friday, August 08, 2008 8:50 AM
To: amber_at_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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