From: Mauricio Carrillo Tripp (trippm_at_wabash.edu)
Date: Tue Jul 06 2004 - 12:43:40 CDT
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
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