Re: COM position

From: Mauricio Carrillo Tripp (trippm_at_wabash.edu)
Date: Tue Jul 06 2004 - 12:12:49 CDT

Hi Michael,

I was trying to avoid what you first suggest if there was
something in NAMD similar to CHARMM's

    ntrfrq 5000 - ! remove translation/rotation of box every 5000 steps

dynamics command. But if this is not possible in NAMD I guess I'll
have to go that way.

Thank you.

Michael Grabe said:
> Mauricio,
>
> I don't know what you are doing, but can't you just
> account for the drift of the COM when you do your
> analysis from the DCD files?
>
> Or you can try to write a TCL pluggin script that
> calculates the COM at certain intervals during the
> run and applies forces to translate the system back
> to the origin. This might be slow though. I don't
> know if time is a problem.
>
> I am not an expert on the TCL plugins but I use
> one that looks for waters in membranes and selectively
> pushes them out. I can send this to you as a starter if
> you think that TCL forces are the way to go.
>
> -Michael
>
> On Jul 6, 2004, at 8:45 AM, 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
>>
>>
> ------------------------------------------------------------------------
> --------------------------
> Michael Grabe, Ph.D.
> Post-doctoral Fellow
> Howard Hughes Medical Institute
> University of California, San Francisco
> 1550 4th Street GD482
> San Francisco, CA 94143
> mgrabe_at_itsa.ucsf.edu
> tel: ++ 415.476.4021
> http://itsa.ucsf.edu/~mgrabe
>
>

-- 
--------------------------------------------------
Mauricio Carrillo Tripp
Chemistry Department
Wabash College
http://chem.acad.wabash.edu/~trippm

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