AMBER Archive (2008)

Subject: AMBER: NAB conjgrad returns error?

From: Carra, Claudio (JSC-SK)[USRA] (claudio.carra-1_at_nasa.gov)
Date: Thu Aug 07 2008 - 10:04:38 CDT

Dear Amber Users,
I got the following problem by trying to run an optimization with NAB.
I'm interested in the parallel version of nmode, but somehow I cannot
manage to reach the end of the optimization.
The input files generated with the same .pdb and leaprc files run
perfectly with sander.
the output is:
 

        mm_options: rgbmax=100.
        mm_options: cut=100.0
        mm_options: ntpr=50
        mm_options: nsnb=999
        mm_options: gb=0
        mm_options: diel=C
      iter Total bad vdW elect nonpolar genBorn
frms
ff: 0 78.42 315.92 -7.44 -230.07 0.00 0.00
2.01e+01
ff: 50 -91.50 169.13 -13.34 -247.29 0.00 0.00
1.30e+00
ff: 100 -105.96 168.14 -12.99 -261.11 0.00 0.00

[...]

ff: 1100 -159.25 166.17 -11.69 -313.73 0.00 0.00
4.10e-01
ff: 1150 -160.14 166.10 -11.66 -314.57 0.00 0.00
3.19e-01
ff: 1200 -160.91 166.42 -12.71 -314.63 0.00 0.00
2.68e-01
ff: 1250 -161.29 166.31 -12.48 -315.12 0.00 0.00
1.78e-01
conjgrad returns 6926336
        mm_options: ntpr=1
ff: 1 -161.38 166.50 -12.30 -315.59 0.00 0.00
9.51e-02
      iter Total bad vdW elect nonpolar genBorn
frms
run.x: sff2.c:1349: ephi2: Assertion `fabs(3.14159 - Phase[atyp]) <
0.01' failed.

-------
here the .nab file. I got part of it from the example aspnb.nab,
which seemed to me a nice example for my problem.
-------
molecule m;
float x[573], fret, ier;

m = getpdb_prm( "snapshot_lig.pdb.3", "leaprc", "", 0 );
readparm(m, "6ssDNA.top");
mm_options("rgbmax=100., cut=100.0, ntpr=50, nsnb=999, gb=0, diel=C");
mme_init( m, NULL, "::z", x, NULL);
setxyz_from_mol(m, NULL, x);

//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 );

//get the normal modes:
nmode( x, 3*m.natoms, mme2, 0, 0, 0.0, 0.0, 0);

--------

thanks a lot in advance for your comments
sincerely
claudio

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