[gmx-users] Restrained EM and cut-offs

David van der Spoel spoel at xray.bmc.uu.se
Tue Apr 30 22:22:33 CEST 2002

On Tue, 30 Apr 2002, Ivano Eberini wrote:

>1) If I use "define = -DPOSRES" and I prepared a posre.itp file, can I 
>run a restrained (cg and steep) EM procedure or this is right just for 
Works fine in EM, just add a potential term.

>2) I read this interesting mail by Bert de Groot, posted on December on 
>gmx-users list:
>"Only for special purposes (like for example a Normal Modes
>type of calculation) you would need to minimize further, but then you
>a) should not use a cut-off (because you get fluctuations in the energies
>because of that and b) should probably move to double precision."
>I installed a copy of GROMACS in double precision, but how can I run EM 
>disabling cut-offs?
set all cutoffs to 0
set nstlist to 0
set pbc = no

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