Re: how to visualize an alchemical FEP transformation??

From: Chris Harrison (charris5_at_gmail.com)
Date: Thu Oct 20 2011 - 15:21:59 CDT

Bruno,

Let's see what we can figure out about your problem; but I'm not
entirely sure I understand your description, ie what are the arms, core
etc. As I understand you have a protein containing Re(CO)3 and you
perform an FEP in which the *entire* Re(CO)3 is made to "vanish." Is
this correct?

You then go on to speak of "arms" that are coordinated to the Re(CO3).
What are these arms? And have you added bonded terms describing their
coordination to the Re(CO3)?

Best,
Chris

--
Chris Harrison, Ph.D.
Theoretical and Computational Biophysics Group
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801
char_at_ks.uiuc.edu                          Voice: 773-570-0329 
http://www.ks.uiuc.edu/~char              Fax:   217-244-6078
Bruno Luís Pinto de Oliveira <boliveira_at_itn.pt> writes:
> Date: Thu, 20 Oct 2011 18:28:13 +0000
> From: Bruno Luís Pinto de Oliveira <boliveira_at_itn.pt>
> To: Axel Kohlmeyer <akohlmey_at_gmail.com>
> CC: "namd-l_at_ks.uiuc.edu" <namd-l_at_ks.uiuc.edu>
> Subject: RE: namd-l: how to visualize an alchemical FEP transformation??
> 
> Dear axel,
> 
> Thank you for your reply. I agree with you. I confess that I still  have some difficulties in understanding what is behind FEP.
> 
> But that´s why I'm studying the FEP principles and trying to understand my results
> 
> All of my group work with TI / Amber and nobody can help me.
> 
> Moreover, in my opinion the NAMD manual is not that well documented in terms of FEP simulations (the only exception is the good tutorial of Chipot et al.) 
> 
> The only possibility I have is asking for "your" help in the forum...
> 
> My doubt is if the Re(CO)3 core disappear during the FEP simulation the "arms" that are coordenated to it will be free/flexible to interact with the protein??? Or when the Re(CO)3 core is vanished what happens is that only the non-bonded terms are switched off?
> 
> I know it is a basic question but I can not find an answer...
> 
> Thank you
> 
> Regards
> 

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