From: Gianluca Interlandi (gianluca_at_u.washington.edu)
Date: Mon Dec 17 2012 - 18:11:01 CST
Thanks for your comment. I decided to use psfgen+alchemify manually
instead. That's an easier route for me. I just wanted to point out this
issue/feature. After all, the mutator plugin issues a warning that one
should always check the structure produced. That's what I did.
Gianluca
On Mon, 17 Dec 2012, JC Gumbart wrote:
> To paraphrase Axel, "and I wished I had a pony".
>
> Feel free to modify the mutator plugin to solve your problem and
> contribute to the greatness of VMD. :)
>
> On Dec 13, 2012, at 4:10 PM, Gianluca Interlandi wrote:
>
>> Dear James,
>>
>> Thanks for your comment. I am not using Alchemify. VMD mutator plugin
>> did everything for me. The problem I have is that the plugin (when the
>> FEP box is checked) replaces both the original side chain and the
>> target side chain in such a way that both (including the original side
>> chain) clash with the backbone of the protein. I attach a snapshot here
>> to illustrate this (the mehionine is mutated into arginine). I wished
>> that the mutator plugin would leave the original side chain in its
>> position (the original conformation was equilibrated for 10 ns). To
>> solve this problem I ended up manually creating my own FEP PDB but I
>> still used the PSF created by the VMD mutator.
>>
>> Gianluca
>>
>> On Thu, 13 Dec 2012, JC Gumbart wrote:
>>
>>> This is irrelevant, because Mutator plus Alchemify make sure that
>>> the correct exclusion list is established so that the end states of your
>>> alchemical transformation never see each other.
>>> This is outdated - recent versions of NAMD (for at least the last couple years?)
>>> automatically generates the exclusions without the need to add them to the psf. I
>>> don't believe there's any need for Alchemify anymore.
>>> On Dec 13, 2012, at 12:47 PM, Chris Chipot wrote:
>>>
>>> Gianluca,
>>> 1) Is it better to use alchemy in NAMD in the FEP or TI mode
>>> for this type of calculatons?
>>>
>>> Contrary to several extraordinary claims (which have never been
>>> supported by extraordinary evidences), there is no real advantage
>>> to use TI over FEP, or the other way around. I would, nonetheless,
>>> advocate FEP for practical reasons -- you can subsequently use
>>> parseFEP for your post-analysis, notably get the BAR estimator.
>>> 2) You describe that in each FEP calculation, 30 intermediate
>>> states were considered. Does this mean that the progress of
>>> lambda was broken down into 30 windows each of 150+150 ps?
>>> How many FEP simulations did you run in total?
>>>
>>> Yes to the first question. I do not quite get the second -- the windows
>>> are chained and the net free-energy change is the sum of free-energy
>>> changes in individual strata.
>>> 3) Do I need to use AlchDecouple on or off?
>>>
>>> I strongly advocate AlchDecouple off, in particular for solvation
>>> free-energy calculations, as one simply cannot assume that the
>>> conformational ensembles in vacuum and in condensed phase
>>> are identical.
>>> 4) The VMD mutator plugin replaces both the wild-type and
>>> mutant side chains such that both clash with the backbone. If
>>> this is a problem, I might create the PDB myself and still
>>> use the PSF generated with VMD.
>>>
>>> This is irrelevant, because Mutator plus Alchemify make sure that
>>> the correct exclusion list is established so that the end states of your
>>> alchemical transformation never see each other.
>>> Sorry, lots of questions. I would appreciate any help on
>>> this!
>>>
>>> Hopefully, I was convincing enough that it will stop here!
>>>
>>> Chris Chipot
>>> --
>>> _______________________________________________________________________
>>> Chris Chipot, Ph.D. Theoretical and Computational Biophysics Group Beckman Institute
>>> University of Illinois at Urbana-Champaign 405 North Mathews Phone: (217) 244-5711 Urbana, Illinois 61801 Fax: (217) 244-6078
>>>
>>> E-mail: chipot_at_ks.uiuc.edu
>>> Christophe.Chipot_at_edam.uhp-nancy.fr
>>> Web: http://www.ks.uiuc.edu/~chipot
>>> http://www.edam.uhp-nancy.fr
>>> The light shines in the darkness, and the darkness has not overcome it.
>>> John 1:5.
>>> _______________________________________________________________________
>>>
>>
>> -----------------------------------------------------
>> Gianluca Interlandi, PhD gianluca_at_u.washington.edu
>> +1 (206) 685 4435
>> http://artemide.bioeng.washington.edu/
>>
>> Research Scientist at the Department of Bioengineering
>> at the University of Washington, Seattle WA U.S.A.
>> -----------------------------------------------------<vwf_dyn_10ns_fep_extr.jpg>
>
>
-----------------------------------------------------
Gianluca Interlandi, PhD gianluca_at_u.washington.edu
+1 (206) 685 4435
http://artemide.bioeng.washington.edu/
Research Scientist at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A.
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