AMBER Archive (2005)

Subject: Re: AMBER: adenine test for LMOD in amber8

From: Istvan Kolossvary (istvan_at_kolossvary.hu)
Date: Thu Jun 16 2005 - 08:16:22 CDT

Dear Giulio,

You are using an old, incomplete LMOD implementation. In the adenine test,
the value of M_LBFGS is set to 1, but it should be 3 or 5. In the latest
LMOD implementation the adenine test has been replaced by two new tests.
Please follow the LMOD link on the Amber home page to obtain the new LMOD.

Hope this helps,

   Istvan

> Dear Amber users and Prof. Kolossvary,
> I have compiled sander (amber8) with the -lmod
> flag on a SGI fuel (./configure -lmod sgi_mips); compilation is fine and
the test.lmod completes successfully.
> However, the adenine.lmod.out significantly differs
> from the adenine.lmod.save file provided with amber8.
> It seems that the .save file is broken, with this error
> message:
> ERROR in load_lbfgs(): YS=0.
> Anyhow, the numbers before the error message are different:
>
>
> --5,17c5,78
> < 2 / 2 E = 0.362285 ( 0.099) Rg = 1.216 rmsd= 0.708
p=1.0000
> < 2 /20 E = 1.73958 ( 0.095) Rg = 1.221 rmsd= 0.307 p=
0.4537
> < 3 /20 E = 5.27472 ( 0.079) Rg = 1.339 rmsd= 1.172 p=
0.0430
> < 3 / 4 E = 1.35929 ( 0.096) Rg = 1.045 rmsd= 1.798 p=
0.5846
> < 9 / 2 E = 0.87711 ( 0.077) Rg = 1.238 rmsd= 0.795 p=
0.8063
> < 9 / 2 E = 1.17001 ( 0.096) Rg = 1.274 rmsd= 1.052 p=
0.6633
> <
> ---------------------------------------------------------------------------
< 2 E = 1.35929 ( 0.096) Rg = 1.045
> < 4 / 5 E = 1.70444 ( 0.090) Rg = 1.299 rmsd= 1.314 p=
0.7945
> < 4 / 3 E = 2.7002 ( 0.084) Rg = 1.169 rmsd= 0.807 p=
0.4090
> < 6 / 5 E = 3.1133 ( 0.099) Rg = 1.057 rmsd= 0.724 p=
0.3106
> < 6 / 8 E = 2.29528 ( 0.080) Rg = 0.994 rmsd= 0.928 p=
0.5358
> < ERROR in load_lbfgs(): YS=0.
> ---
> > 2 / 2 E = 0.457557 ( 0.083) Rg = 1.222 rmsd= 0.734 p=
> 1.0000
> > 2 /20 E = 1.63551 ( 0.084) Rg = 1.217 rmsd= 0.355 p=
> 0.4863
> > 3 / 2 E = 3.53393 ( 0.099) Rg = 1.369 rmsd= 1.100 p=
> 0.1372
> > 3 / 9 E = -4.05462 ( 0.304) Rg = 1.024 rmsd= 2.459 p=
> 1.0000
> > 9 / 2 E = 0.842456 ( 0.088) Rg = 1.236 rmsd= 0.782 p=
> 0.8251
> > 9 / 2 E = 1.2017 ( 0.086) Rg = 1.269 rmsd= 1.052 p=
> 0.6494
> >
> ---------------------------------------------------------------------------
> > 2 E = -4.05462 ( 0.304) Rg = 1.024
> > 4 / 2 E = -6.37122 ( 0.095) Rg = 1.034 rmsd= 0.453 p=
> 1.0000
> > 4 /17 E = -7.37857 ( 0.093) Rg = 1.074 rmsd= 0.968 p=
> 1.0000
> > 6 / 2 E = -6.46066 ( 0.098) Rg = 1.035 rmsd= 0.516 p=
> 1.0000
> > 6 / 2 E = -6.43774 ( 0.084) Rg = 1.030 rmsd= 0.470 p=
> 1.0000
> > 7 / 3 E = -6.476 ( 0.098) Rg = 1.036 rmsd= 0.542 p=
> 1.0000
> > 7 / 2 E = 4.62435 ( 0.093) Rg = 1.095 rmsd= 1.382 p=
> 0.0031

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