[gmx-users] about minimization

David van der Spoel spoel at xray.bmc.uu.se
Fri Mar 22 18:50:08 CET 2002

On Fri, 22 Mar 2002, Alan Wilter Sousa da Silva wrote:

>> Is it possibly a problem with constraints? The default Gromacs parameters
>> will turn bonds into constraints and constrain those using Lincs, also
>> during EM. But for CG/NM type of calculation, the default 4th order for
>> Lincs is not sufficient. In that case, try 8 or 12...
>Gromacs manual p. 33 says (sic) "[...] Conjugate gradient can not be used
>with constraints or freeze groups."  So what LINCS is?  Moreover, is LINCS
>aplied to all system? I mean, including water molecules?  If so, when
>SETTLE is used?

I think this is correct. It will not converge with constraints.

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

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