From: Floris Buelens (floris_buelens_at_yahoo.com)
Date: Mon May 25 2009 - 15:51:16 CDT
Hi Peter,
> I do have one question/concern about your changes... the correction that
> you're applying only works for flat cutoffs, and doesn't apply
> corrections for the switch region (which is part of why my expressions
> were so, erm, 'pretty'). Unless you have some objection, I think I'll
> use the averaging approach that you implemented but keep the actual
> expression for the correction that I was using for water.
Actually yes, I object :-) What I sent you was for switched vdW, it takes the integral for the LJ B^-6 component from rswitch to infinity and subtracts that for the switched region between rswitch and cutoff. I also got some nasty intermediate expressions but after adding everything together and simplifying it all boiled right down to just the (-16 * LJAvgB * numAtoms^2 * PI) / (3 * (rcut+rswitch) ^3) that's in the patch. I was suspicious that it reduced down that far as well but it's stood up to all my scrutiny so far. I'm away at the moment but I can send you my workings next week. (On the other hand, I didn't check if it works with switching off, probably that will need amending).
all the best,
Floris
Hi Floris,
this is, in fact, precisely what I was hoping to implement before I
documented/mainstreamed the tail correction code, but I hadn't yet had
time to through the literature to find an appropriate way to handle
heterogeneous systems (using average vdw parameters made intuitive
sense, but I'd been hoping to find justification for it... fortunately,
you did so and implemented it as well!). I'll play with this a bit and
then get it into the main tree.
I do have one question/concern about your changes... the correction that
you're applying only works for flat cutoffs, and doesn't apply
corrections for the switch region (which is part of why my expressions
were so, erm, 'pretty'). Unless you have some objection, I think I'll
use the averaging approach that you implemented but keep the actual
expression for the correction that I was using for water.
Thanks,
Peter
Floris Buelens wrote:
> Hi Peter,
>
> I've had a go at a long range dispersion correction, patch is attached. It's the same idea as your water tail correction but it derives an average dispersion coefficient from the whole system rather than only considering water. Also my final expression comes out less visually arresting than yours :-) Using an average dispersion coefficient reduces to the same thing for pure water and is formally correct for any homogeneous mixtures wher g(r) approaches 1 for r > rswitch. I think it's not quite as clear-cut for non-homogeneous protein-water systems but in my opinion it's still better than not applying any correction to the pressure (Shirts et al., J Phys Chem B. 2007 111:13052 convinced me I should be doing this for binding free energy work).
> I haven't tested it extensively but I replicated table 1 of the Shirts et al paper (density of pure TIP3P water with PME is no longer sensitive to cutoff) and showed the corrected single point LJ energy for a 900-TIP3P box is stable beyond ~7A while the uncorrected energy approaches the same value asymptotically out to >20A.
> I hope it's of some use and that something along these lines ends up in NAMD in the future?
> Best wishes,
>
> Floris
>
>
>
> ----- Original Message ----
> From: Peter Freddolino <petefred_at_ks.uiuc.edu>
> To: Floris Buelens <floris_buelens_at_yahoo.com>
> Cc: namd-l_at_ks.uiuc.edu
> Sent: Wednesday, 29 April, 2009 16:26:24
> Subject: Re: namd-l: water tail correction
>
> To answer the rest of your question (since I realized I didn't do so
> before, sorry), the current implementation should work for any
> combination of switching/cutoff schemes and water models, since it reads
> the former from your simulation parameters and explicitly pulls the VDW
> parameters that it needs from the first water molecule in your structure.
> Best,
> Peter
>
> Floris Buelens wrote:
>> Hi Peter,
>>
>> I notice that NAMD 2.7b1 contains an implementation of water tail corrections for energy and pressure - can you give some more details? Is this comparable to the GROMACS dispersion correction scheme? Is this ready for use? Is it general in scope (i.e. independent of water model and cutoff / switching scheme)?
>> thanks a lot,
>>
>> Floris
>>
>>
>>
>
>
>
>
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