[gmx-users] Making covalent bonds between protein subunits

[David van der Spoel]

On Thu, 25 Oct 2001, K.A.Feenstra wrote:

>> an alternative solution: Instead of specifying new covalent bonds, you could define *distance restraints* on the calcium and monomer atoms (see
>> GROMACS manual). These are, roughly speaking, also harmonic potentials. Maybe they work better.
>
>Two remarks:
>1) depending on the parameters, distance restraints can be exactly harmonic potentials.
>2) bonds usually are *not* represented by harmonic potentials, but by constraints
>   (don't confuse constraint and restraint, a constraint is a fixed distance w/o potential).
>But, I would think Volkers' suggestion is a good one (let's hope it works).
I'm afraid not, the distance restraints still have to be within the
molecule in GROMACS definition.


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
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++