Re: SMD vs RAMD / TMD

From: Vlad Cojocaru (Vlad.Cojocaru_at_eml-r.villa-bosch.de)
Date: Fri Jan 25 2008 - 04:00:10 CST

Dear Samuel,

You maybe misunderstood what I said... RAMD was (is) designed to search
for exit routes for small molecules from buried active sites. It can
also be used for protein-protein docking but I do not see how one can
adapt it to drive the transition between two conformations of a protein
chain.

Best
vlad

Samuel Morales Navarro wrote:

>Hello!!
>
>For my undergraduate thesis, I´m studying the activation mechanism of
>potassium plant channel. The experimental results, propose that a segment of
>the channel, adopts two conformations, and to simulate them, one of the
>possibilities is TMD (targeted molecular dynamics), where of an initial
>structure, applying a force, it reach a final structure. My problem so far,
>is that I haven´t this final structure.
>You says what the "RAMD method is useful for finding pathways", that is
>precisely for what I want to know. You might give me more details of the
>method and how might apply it to simulate the states of the channel?.. You
>might give me references of the method?
>
>I hope a soon response and appreciating your help;
>
>_______________________________
>Samuel Morales Navarro
>Licenciado en Bioquímica
>Pontificia Universidad Católica de Chile
>Centro de Bioinformática y Simulación Molecular
>Universidad de Talca
>http://cbsm.utalca.cl/
>
>"...For God so loved the world that he gave his one and only Son, that
>whoever believes in him shall not perish but have eternal life..." John 3.16
>
>-----Mensaje original-----
>De: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] En nombre de
>Vlad Cojocaru
>Enviado el: Jueves, 24 de Enero de 2008 15:29
>Para: Francesco Pietra
>CC: NAMD list
>Asunto: Re: namd-l: SMD vs RAMD
>
>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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-- 
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Dr. Vlad Cojocaru
EML Research gGmbH
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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/
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