From: Radak, Brian K (bradak_at_anl.gov)
Date: Wed Apr 12 2017 - 13:17:46 CDT
Yes, you should only neutralize one endpoint (if that also neutralizes the other, that's just a bonus).
I should also note that alchemy in NAMD is essentially only implemented with PME - you cannot use implicit solvent.
Brian Radak
Postdoctoral Appointee
Leadership Computing Facility
Argonne National Laboratory
9700 South Cass Avenue, Bldg. 240
Argonne, IL 60439-4854
(630) 252-8643
brian.radak_at_anl.gov
________________________________________
From: djhuggins_at_gmail.com [djhuggins_at_gmail.com] on behalf of David Huggins [djh210_at_cam.ac.uk]
Sent: Wednesday, April 12, 2017 1:05 PM
To: Radak, Brian K
Cc: namd-l_at_ks.uiuc.edu
Subject: Re: namd-l: Neutralize a box for FEP
Thanks Brian,
Do you mean that counterions should be added to neutralize just one of
the charges (-1 charge added)?
I should clarify that I am not using PME as I found it incompatible
with my alchemified structures.
Best wishes,
Dave
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Dr David J. Huggins
University of Cambridge
Department of Chemistry
Lensfield Rd
Cambridge
CB2 1EW
United Kingdom
Phone: +44 (0)1223 763854
Email: djh210_at_cam.ac.uk
Web: http://huggins-lab.tcm.phy.cam.ac.uk/
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
On 12 April 2017 at 17:14, Radak, Brian K <bradak_at_anl.gov> wrote:
> Dave,
>
> NAMD performs rigorous PME at both endpoints - all calculations involving A and B will be conducted without any knowledge of the other (yes, this means there are two energy/force computations per step).
>
> The alchDecouple keyword has puzzling syntax IMO. "alchDecouple off" means that _all_ nonbonded interactions with each alchemical group are scaled by the appropriate lambda factor. "alchDecouple on" means that non-bonded interactions _between alchemical atoms of the same group_ are _never_ scaled. The latter requires additional PME calculations (up to 5 total I think?), but these are very small systems with low cost. This might exacerbate PME artifacts for charged systems, since you have to introduce additional neutralizing plasma terms, but I've never used "alchDecouple on", so I have no data to base that assertion on.
>
> Cheers,
> Brian
>
> Brian Radak
> Postdoctoral Appointee
> Leadership Computing Facility
> Argonne National Laboratory
>
> 9700 South Cass Avenue, Bldg. 240
> Argonne, IL 60439-4854
> (630) 252-8643
> brian.radak_at_anl.gov
>
> ________________________________________
> From: owner-namd-l_at_ks.uiuc.edu [owner-namd-l_at_ks.uiuc.edu] on behalf of David Huggins [djh210_at_cam.ac.uk]
> Sent: Wednesday, April 12, 2017 10:30 AM
> To: namd-l_at_ks.uiuc.edu
> Subject: namd-l: Neutralize a box for FEP
>
> Dear All,
>
> I am interested in the correct way to neutralize a box in which a
> charged molecule A is mutated by FEP into a molecule B with the same
> charge.
>
> Lets say A and B both have a charge of +1. Should counterions be added
> to neutralize just one of the charges (-1 charge added) or both
> charges (-2 charge added)?
>
> My guess is that the former is correct, but it may be an issue that
> the decoupled atoms interact with their periodic images. Does
> alchDecouple then need to be set to off?
>
> Thanks,
>
> Dave
>
>
>
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>
> Dr David J. Huggins
> University of Cambridge
> Department of Chemistry
> Lensfield Rd
> Cambridge
> CB2 1EW
> United Kingdom
>
> Phone: +44 (0)1223 763854
> Email: djh210_at_cam.ac.uk
> Web: http://huggins-lab.tcm.phy.cam.ac.uk/
>
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>
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