[gmx-users] Re:

David van der Spoel spoel at xray.bmc.uu.se
Thu Nov 29 13:03:52 CET 2001

On Thu, 29 Nov 2001, Erik Lindahl wrote:

>> I'm a french student using Gromacs 2.0, and I've a problem with distance
>> restrain between 2 atoms.
>> I am in the case I need in my simulation that 2 atoms must stay close to each
>> other at a distance of 2 Angstrom, with a strenght equal to a covalent bond...
>> Actually, I proceed in this way:
>> I modify the .top file before the last RUN (ie after minimisation steps) by
>> writing the lines:
why don't you define a real bond then? Of course this depends on the
nature of the bond, but e.g. protein/heme bonds can be made automatically
by editing the file containing so-called special bonds (specbond.dat)

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