From: Brian Bennion (brian_at_youkai.llnl.gov)
Date: Tue Jul 06 2004 - 12:11:28 CDT
Hi Mauricio,
Control of the center of mass motion is very difficult to do in any
ensemble, although NVE is probably the best regime to work in.
That said, you can "align" all the frames from your trajectory within VMD
and do analysis there. Here translation and rotation effects are
accounted for with pretty good accuracy.
I too have been dismayed by the lack of momentum conservation within NAMD.
Brian
On Tue, 6 Jul 2004, Mauricio Carrillo Tripp wrote:
>
> Hi Marc, thanks for the reply
>
> I was aware of the COMmotion command, but this will only affect the initial
> step. What I need to do is to allways keep it in the same position. I was
> using
> Langevin for temperature control but this would make the COM move a lot,
> so I changed to Vel. Reassigment but it's still moving (not as much as before
> though), but because of the analisys I want to make I need it to be still.
> Do you
> know if there's an easy way to do this?
>
>
> Kamp, Marc vander said:
> > Hi Mauricio,
> >
> > Did you also read this in the user guide:
> >
> > COMmotion < allow center of mass motion? >
> >
> > Acceptable Values: yes or no
> >
> > Default Value: no
> >
> > Description: Speci es whether or not motion of the center of mass of the
> > entire system
> >
> > is allowed. If this option is set to no, the initial velocities of the
> > system will be adjusted to
> >
> > remove center of mass motion of the system. Note that this does not
> > preclude later centerof-
> >
> > mass motion due to external forces such as random noise in Langevin
> > dynamics, boundary
> >
> > potentials, and harmonic restraints.
> >
> > (p.46 in the pdf)
> >
> > Marc
> >
> >
> >
> > -----Original Message-----
> > From: owner-namd-l_at_ks.uiuc.edu on behalf of Mauricio Carrillo Tripp
> > Sent: Mon 5-7-2004 21:47
> > To: namd-l_at_ks.uiuc.edu
> > Cc:
> > Subject: namd-l: COM position
> >
> >
> >
> >
> > Hi all, I'm not sure this went through last time (I haven't got any
> > replies) , so I'm sending it again with more coments...
> >
> > Is there a way to keep the system's center of mass position fixed at a
> > certain point (e.g. origin) ?
> > is there a command in NAMD to accomplish this or do I have to write a
> > script? How do I do it?
> >
> > Reading the manual I found in section 6.7.3 and 6.7.6 (Options for
> > conformational
> > restraints and Examples, Fixed restraints page 80) that I can do
> > something
> > like
> >
> > urestrain {
> > posi group {(*,*,*)} kf=20 ref=(0,0,0)
> > }
> >
> > I'm not sure about the *'s though, should I use {all} instead?
> > Would this work?
> >
> > Afterall, all I want to do is to keep the COM from moving in the Z
> > direction... it should be something quite simple, but I'm not sure
> > how to do it.
> >
> > Thanks for any help
> >
> >
> > --------------------------------------------------
> > Mauricio Carrillo Tripp
> > Chemistry Department
> > Wabash College
> > http://chem.acad.wabash.edu/~trippm
> >
> >
> >
> >
>
>
> --
> --------------------------------------------------
> Mauricio Carrillo Tripp
> Chemistry Department
> Wabash College
> http://chem.acad.wabash.edu/~trippm
>
*****************************************************************
**Brian Bennion, Ph.D. **
**Computational and Systems Biology Division **
**Biology and Biotechnology Research Program **
**Lawrence Livermore National Laboratory **
**P.O. Box 808, L-448 bennion1_at_llnl.gov **
**7000 East Avenue phone: (925) 422-5722 **
**Livermore, CA 94550 fax: (925) 424-6605 **
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