Re: Fwd: Re: SMD vs RAMD

From: Vlad Cojocaru (Vlad.Cojocaru_at_eml-r.villa-bosch.de)
Date: Fri Jan 25 2008 - 03:37:46 CST

Dear Francesco,

Yes its true.. RAMD works for now only with AMBER 8 which is a drawback
.. The person who wrote the code is not in our lab anymore and I am not
experienced with fortran so until somebody will be interested in porting
the RAMD patch to AMBER 9 (or future versions of AMBER), we are stucked
to AMBER8. I dont know whether there is a chance that the RAMD will be
included in the next standard AMBER distribution (AMBER10) ...

As for the NAMD implementation .... I've heard some people have done
that already. NAMD has a very powerful feature which is tclforces. In a
similar fashion as ABF was implemented in NAMD via a tcl script, RAMD
can be implemented as well .... It just requires some time. I was
planning to attempt to do that but it seems that other people have done
it already. Maybe we can hope that the tcl script will be available (as
the ABF is) as soon as one study using RAMD in NAMD will be published (I
am not aware of any publication thus far). Otherwise, I am still
considering writing it but as I said it requires some time and also
extensive testing .... Of course, if you are experienced with tcl you
can attempt yourself ...

Best of luck
vlad

Francesco Pietra wrote:

>I forgot to add that Amber 9 and OpenMPI 1.2.3 are compiled with Intel.
>
>--- Francesco Pietra <chiendarret_at_yahoo.com> wrote:
>
>
>
>>Date: Thu, 24 Jan 2008 12:29:07 -0800 (PST)
>>From: Francesco Pietra <chiendarret_at_yahoo.com>
>>Subject: Re: namd-l: SMD vs RAMD
>>To: Vlad Cojocaru <Vlad.Cojocaru_at_eml-r.villa-bosch.de>
>>
>>Vlad:
>>You made the difference quite clearly. Thanks.
>>
>>I have a personal license for Amber 9, though I found it difficult to get
>>Amber
>>8, for which version has the Wade's group adapted RAMD.
>>
>>That explains my question on NAMD mailing list. I have planned to install
>>NAMD
>>anyway to work with Amber's prmtop/inpcrd (as I have no CHARMM), if not else
>>to
>>add to the possibilities offered by Amber. It would be wonderful if RAMD can
>>be
>>run from NAMD. Actually, I am not in a hurry as I am still at MD with my
>>protein and its large non-polymeric ligand, so that the machine is not
>>available immediately for installations.
>>
>>A protocol on how to compile RAMD + NAMD would be very welcome. I am at
>>Debian
>>Linux amd64 dual opterons shared memory. As parallelization support I use
>>OpenMPI 1.2.3. Basically I am an experimental organic chemist, so that my
>>know
>>how as system maintainer is limited.
>>
>>Regards
>>francesco
>>
>>
>>
>>
>>
>>--- Vlad Cojocaru <Vlad.Cojocaru_at_eml-r.villa-bosch.de> wrote:
>>
>>
>>
>>>Hi Francesco,
>>>
>>>As I am working with RAMD, I might be able to answer your question. In
>>>RAMD, a random force is added on the COM of the ligand for N MD steps.
>>>After N steps, the movement of the ligand is assessed against a
>>>user-defined threshold. if the distance d between the COM position
>>>before and after the N steps is higher than the threshold, the same
>>>force will be applied for the next N steps. However, if d is lower than
>>>the threshold, the direction of the force will be changed. Therefore,
>>>during a RAMD run you will have a lots of different force directions
>>>generated before the ligand goes out. Therefore, you dont need to know a
>>>priori the ligand release path. The method is useful for finding pathways
>>>
>>>In SMD, the direction of the applied force is known a priori and the
>>>ligand is pulled in that direction during the whole simulation. The
>>>method is useful for getting the force profile for the ligand release
>>>via the defined pathway (or the free energy profile if combined with
>>>Jarzynski's equality). Details about SMD are very nicely covered in the
>>>NAMD documentation (references to the original papers are also there).
>>>
>>>If you have further question about the use of RAMD, please contact me.
>>>
>>>Best
>>>vlad
>>>
>>>
>>>
>>>Francesco Pietra wrote:
>>>
>>>
>>>
>>>>As far as I can understand from descriptions (not having installed NAMD
>>>>
>>>>
>>>yet),
>>>
>>>
>>>>Steered Molecular Dynamic (SMD) in NAMD is capable to apply an external
>>>>
>>>>
>>>force
>>>
>>>
>>>>to a part of the system. Is that possible through SMD to apply a randomly
>>>>generated force to the center of mass of a portion of the system, may be
>>>>
>>>>
>>>that a
>>>
>>>
>>>>non-polymeric (drug-like) ligand of a protein to pull the ligand out and
>>>>
>>>>
>>>follow
>>>
>>>
>>>>the path?
>>>>
>>>>Again, as far as I can understand from descriptions, that action should be
>>>>possible with RAMD (Randomly Accelerated Molecular Dynamics) from Prof
>>>>
>>>>
>>Wade
>>
>>
>>>>group.
>>>>
>>>>Has anyone experience in comparing the two approaches?
>>>>
>>>>Thanks
>>>>francesco pietra
>>>>
>>>>
>>>>
>>>>
>>>>
>____________________________________________________________________________________
>
>
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>>>
>>>>
>>>>
>>>>
>>>>
>>>--
>>>
>>>
>>>
>>----------------------------------------------------------------------------
>>
>>
>>>Dr. Vlad Cojocaru
>>>
>>>EML Research gGmbH
>>>Schloss-Wolfsbrunnenweg 33
>>>69118 Heidelberg
>>>
>>>Tel: ++49-6221-533266
>>>Fax: ++49-6221-533298
>>>
>>>e-mail:Vlad.Cojocaru[at]eml-r.villa-bosch.de
>>>
>>>http://projects.villa-bosch.de/mcm/people/cojocaru/
>>>
>>>
>>>
>>>
>>----------------------------------------------------------------------------
>>
>>
>>>EML Research gGmbH
>>>Amtgericht Mannheim / HRB 337446
>>>Managing Partner: Dr. h.c. Klaus Tschira
>>>Scientific and Managing Director: Prof. Dr.-Ing. Andreas Reuter
>>>http://www.eml-r.org
>>>
>>>
>>>
>>----------------------------------------------------------------------------
>>
>>
>>>
>>>
>>>
>>
>>
>>
>>
>>
>____________________________________________________________________________________
>
>
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>>
>>
>>
>
>
>
> ____________________________________________________________________________________
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>
>

-- 
----------------------------------------------------------------------------
Dr. Vlad Cojocaru
EML Research gGmbH
Schloss-Wolfsbrunnenweg 33
69118 Heidelberg
Tel: ++49-6221-533266
Fax: ++49-6221-533298
e-mail:Vlad.Cojocaru[at]eml-r.villa-bosch.de
http://projects.villa-bosch.de/mcm/people/cojocaru/
----------------------------------------------------------------------------
EML Research gGmbH
Amtgericht Mannheim / HRB 337446
Managing Partner: Dr. h.c. Klaus Tschira
Scientific and Managing Director: Prof. Dr.-Ing. Andreas Reuter
http://www.eml-r.org
----------------------------------------------------------------------------

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