Re: Constraints in NAMD

From: Jerome Henin (jhenin_at_cmm.chem.upenn.edu)
Date: Wed Apr 22 2009 - 10:30:44 CDT

Hi Dimitry,

> 1/ I want to make en energy minimization and then apply restraints.
> Does that mean that I can not do this in a single run - first I have
> to do the EM, then acquire resulting pdb file and only then start a
> new simulation specifying this file as the reference one?

I think that is correct, yes.

> 2/ What is the format of consref and conskfile files? I could not find
> any examples of the files on the web - only the config file options.
> Can you show me yours?

Only if you show us yours first, of course.
In any case, they are plain PDB files containing all atoms in the
system. The one for force constants has kx, ky and kz where x, y and z
ought to be (some of these constants may be zero). The easiest way to
make it is to use VMD.

> 3/ I want to gradually decrease the restraints on my atoms. Could I do
> this in a single run?

Yes: using constraintScaling repeatedly between several "run" statements.

> 4/ What value is the general maximum for force constraint in NAMD? I
> mean, for example in gromacs setting posres constant to more than 1000
> kJ/mol nm is generally useless since nothing moves already at this
> value.

Physics in NAMD is roughly the same as in Gromacs (well, most release
versions of Gromacs anyway). Just divide everything by 4.184, then
multiply by 10 (or 100, or sometimes the other way around), and you're
good to go.

Cheers,
Jerome

PS: the Gromacs physics thing is just a joke, of course. Erik, David,
Berk, Gerrit, if you read this: sorry, couldn't resist, no offense
meant.

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