[gmx-users] about minimization

David van der Spoel spoel at xray.bmc.uu.se
Fri Mar 22 00:50:19 CET 2002

On Thu, 21 Mar 2002, hugo verli wrote:

>sorry if I am introducing problems already discussed before in this list. But I
>wasn`t able to resolv it yet and I did not found teh answer in the list files. I
>read some references in wich the gradient used to normal mode analysis is under
>10e-5 kcal. But I cannot achieve gradient under 10e+2 kj, neither with steepest
>descents or with conjugated gradients. I reproduced these erros and one answer
>here. But I am working with double precision so the problem still exist. I also
>tried to minimize another system (I choosed the speptide.pdb from gromacs
>tutorial). The error with this structure is the same. Could these errors be dued
>to my machine or am I doing something wrong? 

I have looked into this last week or so, and it may be that something is 
wrong with the conjugate gradients minimizer. I haven't found the real 
problem yet.

Groeten, David.
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel

More information about the gromacs.org_gmx-users mailing list