From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Sun Dec 16 2012 - 19:24:25 CST
This is not a exactly a problem with the exclusions. The problem is that NAMD looks for parameters BEFORE auto-generating the exclusions. So it tries to find a parameter that it will never need, and then complains when it can't.
I raised this issue a couple years ago, but I guess it never got fixed.
On Dec 14, 2012, at 7:07 PM, Gianluca Interlandi wrote:
> I found that I DO need to use alchemify explicitly if I use psfgen instead of the mutator plugin. I am using NAMD2.9 and during minimization it complained of not funding angle parameters for CBA-CA-CBB. This is because the PSF generated by psfgen included that angle. So, I ran alchemify on it and minimization is running fine now.
>
> The alchemify website says (http://www.edam.uhp-nancy.fr/Alchemify/):
>
> "As of NAMD 2.7b2, alchemify is not needed anymore, since all unwanted
> terms are discarded by NAMD at runtime."
>
> This does not seem to be true, at least not for minimization. Or, could it be that I'm using a binary compiled with the memory optimized option? How do I find that out? I'm using "NAMD_2.9_Linux-x86_64".
>
> In any case, I ran alchemify also on the solvated and ionized structure just to be sure that the nonbonded exclusion list is created and taken into account.
>
> Thanks,
>
> 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 This is outdated - recent versions of NAMD (for at least the last couple years?)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.
> -----------------------------------------------------
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