Prof. Case thanks for the corrections.
About my opinion the dgrad=0.1 value from the conjgrad settings is big:
conjgrad(x,3*m.natoms,fret,mme,0.1,0.001,2000);
I would try:
dgrad=0.005;
conjgrad( x, 3*m.natoms, fret, mme, dgrad, 0.1, 3000);
and for Newton-Raphson:
mm_options( "ntpr=1" );
dgrad=1.e-12;
newton( x, 3*m.natoms, fret, mme, mme2, dgrad, 0.0, 2000);
This usually works for me.
R.
2013/4/3 Rasha Alqus <rasha.alqus.manchester.ac.uk>
> I have aproblem frequancy dosent appear in the .out file. This is the nab
> file and the .out .
> WHAT IS THE PROBLEM
>
>
> NAB FILE
>
> mlecule m;
> float x[1080], fret;
> m = getpdb("G17-vac-min.pdb");
> readparm(m, "G17-vac.top");
> getxyz("G17-vac-min.rst",360,x);
> mm_options("cut=999, ntpr=10, nsnb=99999, diel=C, gb=0, dielc=1.0");
> mme_init(m, NULL, "::Z", x, NULL);
> setxyz_from_mol(m, NULL, x);
> //conjugate gradient minimization
> conjgrad(x,3*m.natoms,fret,mme,0.1,0.001,2000);
> //newton-raphson minimization
> newton(x,3*m.natoms,fret,mme,mme2,0.00000001,0.0,6);
> //get normal modes
> nmode(x,3*m.natoms,mme2,50,0,0.0,0.0,0);
>
> THIS IS THE .OUT FILE
>
> Reading parm file (G17-vac.top)
> title:
> default_name
> mm_options: cut=999
> mm_options: ntpr=10
> mm_options: nsnb=99999
> mm_options: diel=C
> mm_options: gb=0
> mm_options: dielc=1.0
> iter Total bad vdW elect nonpolar genBorn
> frms
> ff: 0 1298.51 153.56 -29.89 1174.84 0.00 0.00
> 1.64e+00
> ff: 10 1289.14 126.48 -18.30 1180.97 0.00 0.00
> 1.46e+00
> ff: 20 1284.56 122.48 -14.31 1176.40 0.00 0.00
> 6.95e-01
> ff: 30 1281.18 124.37 -12.39 1169.20 0.00 0.00
> 6.00e-01
> ff: 40 1279.68 124.22 -12.47 1167.93 0.00 0.00
> 4.54e-01
> ff: 50 1278.86 121.54 -10.55 1167.87 0.00 0.00
> 4.25e-01
> ff: 60 1277.84 121.02 -9.61 1166.43 0.00 0.00
> 3.47e-01
> ff: 70 1277.24 123.18 -9.26 1163.32 0.00 0.00
> 2.32e-01
> ff: 80 1276.75 121.92 -7.15 1161.98 0.00 0.00
> 3.24e-01
> ff: 90 1276.09 123.96 -6.85 1158.98 0.00 0.00
> 4.25e-01
> ff: 100 1275.24 124.28 -6.61 1157.56 0.00 0.00
> 4.94e-01
> ff: 110 1274.70 124.50 -5.98 1156.19 0.00 0.00
> 3.24e-01
> ff: 120 1274.13 126.18 -6.21 1154.16 0.00 0.00
> 2.85e-01
> ff: 130 1273.88 127.44 -6.69 1153.13 0.00 0.00
> 3.19e-01
> ff: 140 1273.58 127.06 -6.45 1152.97 0.00 0.00
> 4.03e-01
> ff: 150 1273.34 126.00 -6.14 1153.48 0.00 0.00
> 2.41e-01
> ff: 160 1273.04 125.90 -6.20 1153.35 0.00 0.00
> 2.70e-01
> ff: 170 1272.78 125.25 -6.73 1154.27 0.00 0.00
> 2.31e-01
> ff: 180 1272.61 124.21 -6.56 1154.95 0.00 0.00
> 2.20e-01
> ff: 190 1272.42 123.50 -6.62 1155.53 0.00 0.00
> 2.84e-01
> ff: 200 1272.23 123.47 -6.75 1155.51 0.00 0.00
> 1.95e-01
> ff: 210 1272.03 123.62 -6.64 1155.05 0.00 0.00
> 1.79e-01
> ff: 220 1271.85 123.95 -6.76 1154.66 0.00 0.00
> 1.57e-01
> ff: 230 1271.71 124.18 -7.33 1154.86 0.00 0.00
> 1.61e-01
> ff: 240 1271.55 124.09 -7.77 1155.23 0.00 0.00
> 1.41e-01
> ff: 250 1271.35 125.78 -7.90 1153.47 0.00 0.00
> 1.62e-01
> ff: 260 1271.12 126.42 -6.96 1151.66 0.00 0.00
> 1.72e-01
> ff: 270 1270.92 126.16 -6.22 1150.98 0.00 0.00
> 2.09e-01
> ff: 280 1270.63 127.67 -6.38 1149.34 0.00 0.00
> 2.72e-01
> ff: 290 1270.42 127.99 -6.58 1149.00 0.00 0.00
> 1.75e-01
> ff: 300 1270.17 127.14 -6.11 1149.15 0.00 0.00
> 1.73e-01
> ff: 310 1269.93 127.17 -6.08 1148.85 0.00 0.00
> 1.87e-01
> ff: 320 1269.73 127.95 -6.57 1148.35 0.00 0.00
> 2.14e-01
> ff: 330 1269.49 127.12 -6.66 1149.03 0.00 0.00
> 2.06e-01
> ff: 340 1269.29 126.30 -7.14 1150.13 0.00 0.00
> 1.69e-01
> ff: 350 1269.17 126.07 -7.53 1150.64 0.00 0.00
> 1.20e-01
> ff: 360 1269.07 125.54 -7.66 1151.19 0.00 0.00
> 1.45e-01
> ff: 370 1268.96 125.33 -8.00 1151.63 0.00 0.00
> 1.47e-01
> ff: 380 1268.86 125.29 -8.45 1152.02 0.00 0.00
> 1.20e-01
> ff: 390 1268.77 125.33 -8.77 1152.21 0.00 0.00
> 1.06e-01
> ff: 400 1268.69 126.00 -8.93 1151.62 0.00 0.00
> 9.27e-02
> iter Total bad vdW elect nonpolar genBorn
> frms
> ff: 1 1268.69 126.00 -8.93 1151.62 0.00 0.00
> 9.27e-02
> adding 0.00000 to diagonal of the hessian
> rms of search direction: 0.0927305
> For alpha = 0.00000 energy = 1268.6914815643
> For alpha = 1.00000 energy = 4943.5463474506
> For alpha = 0.00127 energy = 1268.6855629069
> For alpha = 0.00128 energy = 1268.6855629107
> adding 0.00000 to diagonal of the hessian
> rms of search direction: 0.0899483
> For alpha = 0.00000 energy = 1268.6855629107
>
>
> ________________________________________
> From: Deák Robert [kokumetto.gmail.com]
> Sent: 03 April 2013 14:11
> To: AMBER Mailing List
> Subject: Re: [AMBER] vecs file
>
> The frequencies are at the end of the .out file, after the minimization
> info.
>
> Regards,
> R.
>
>
> 2013/4/3 Rasha Alqus <rasha.alqus.manchester.ac.uk>
>
> > How do i obtain the vibrational frequancy from these results
> >
> > ________________________________________
> > From: Deák Robert [kokumetto.gmail.com]
> > Sent: 03 April 2013 13:44
> > To: AMBER Mailing List
> > Subject: Re: [AMBER] vecs file
> >
> > 1080 means: you have 360 atoms in the analyzed system, so 1080
> coordinates.
> > After this number, the vecs file contains the components of the normal
> mode
> > vectors, where each vector has 1080 coordinates.
> > So after every 1080 numbers begins the next normal vector.
> >
> > Regards
> >
> >
> > 2013/4/3 Rasha Alqus <rasha.alqus.manchester.ac.uk>
> >
> > > Dear AMBER USERS,
> > >
> > >
> > >
> > > what dose the columns in vecs file represents . I ran a nmode to
> > > calculate the vibrational frequency.
> > >
> > > Regards
> > >
> > >
> > >
> > >
> > >
> > > this is apart of vecs file
> > >
> > >
> > >
> > > modes from NAB
> > > 1080
> > > 1.72151 -0.01058 0.03683 0.80188 -0.25366 -0.09737
> > > 0.05862
> > > 0.95776 -0.14852 0.09006 1.36019 -1.16153 0.65775
> > > 1.91388
> > > .
> > >
> > > .
> > >
> > > .
> > >
> > > .
> > >
> > > .
> > >
> > > .
> > >
> > >
> > >
> > >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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Received on Thu Apr 04 2013 - 06:00:03 PDT
