AMBER Archive (2007)

Subject: Re: AMBER: restraining atoms

From: Thomas Cheatham III (tec3_at_utah.edu)
Date: Mon May 14 2007 - 12:27:01 CDT

> In my simulation , although I am able t restrain atoms but it seems to me as
> if only first group of atoms is bein restrained and not all. can somebody
> clear my doubt whether only first group of atoms, following thr restrain
> command gets fixed or all?
>
> I have attached my input script and i feel as if only 10-20 atoms are
> restrained and not 25,26,28-38 atoms.

The output file (mdout) lists what atoms are being restrained; please
refer to this to see if the atoms are being selected appropriately. Also
note that an alternative syntax (if the above is not being parsed
correctly) would be

restraintmask = '@10-20 | @25 | @26 | @28-38'

Finally, the atoms will not be "fixed" or constrained but restrained, i.e.
there will be force to move them back to the desired position...

--tec3
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