From: Jérôme Hénin (jhenin_at_ifr88.cnrs-mrs.fr)
Date: Mon Mar 19 2012 - 11:33:16 CDT
Something very similar can be achieved using the collective variables
module. There are no positional restraints, but you can enforce an
RMSD restraint and have the force constant change linearly over time.
The RMSD restraint could be changed to a true positional restraint
with a minor change in the code (making the coordinate alignment
optional), which I don't have time to do now but can look at later if
you are interested. I intended to make that change eventually anyway.
You may also apply a restraint to three coordinates at once: the RMSD,
center-of-mass position, and rotation of the protein. Everything
should be in the user's guide and list archives, but let us know if
you need help with this.
On 19 March 2012 16:33, Albert <mailmd2011_at_gmail.com> wrote:
> hello thanks a lot for kind reply.
> I mean eg:
> force constant on backbone was removed over 20 ns from 10 Kcal/mol.A^2 --->
> 0 Kcal/mol.A^2 linearly
> 2012/3/19 Axel Kohlmeyer <akohlmey_at_gmail.com>
>> On Mon, Mar 19, 2012 at 9:29 AM, Albert <mailmd2011_at_gmail.com> wrote:
>> > Hello:
>> > I've got a membrane protein system and I would like to strip off the
>> > restrain on protein backbone linearly. I am wondering is it possible to
>> > do
>> > so in NAMD?
>> please explain what you mean by "strip off linearly".
>> > thank you very much
>> > best
>> > Albert
>> Dr. Axel Kohlmeyer
>> akohlmey_at_gmail.com http://goo.gl/1wk0
>> College of Science and Technology
>> Temple University, Philadelphia PA, USA.
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