From: Brian Bennion (brian_at_youkai.llnl.gov)
Date: Tue Jul 06 2004 - 12:50:52 CDT
If you are genuinely tied to NAMDs routines then perhaps a crazy thing
like running the trajectory through VMD to align the membrane and then
write out a new dcd file...
just my 2 cents
brian
On Tue, 6 Jul 2004, Mauricio Carrillo Tripp wrote:
>
> Hi Brian,
>
> What I'm doing is trying to calculate the pressure profile along the normal
> of a lipid bilayer using NAMD's routines. So I have to do the analisys
> within NAMD. I was trying to find out a way to translate the entire system
> every number of steps to keep the membrane at a fixed spatial location,
> otherwise I get very noisy profiles.
>
> Any ideas?
>
> Thank you.
>
> Brian Bennion said:
> > 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 **
> > *****************************************************************
> >
>
>
> --
> --------------------------------------------------
> 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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