On Wed, Apr 6, 2016 at 8:37 PM, Neha Gandhi <n.gandhiau.gmail.com> wrote:
> Dear List,
>
> Recently literature indicates preference for using CHARMM22* force field
> (its ability to produce NMR observable) for simulations of intrinsically
> disordered proteins. This force field is either available in gromacs or
> ACEMD package.
>
> I am interested in simulating an IDP peptide with CHARMM22* force field and
> advanced sampling techniques in AMBER. The use of pmemd.cuda will further
> scale the simulations very well. However, AMBER does not support any
> switching or shifting method for LJ interactions.
>
> I read paper on CHARMM-GUI where a hard-truncation method is used for
> simulations of membrane in AMBER using CHARMM36 force field. Can I use a
> similar protocol in AMBER to simulate IDP (without membrane) or I have to
> consider some other parameters while using CHARMM22* force field in AMBER?
>
As I understand it, the force shifting method is required to reproduce
reference CHARMM results for a couple kinds of lipids. Other types of
systems display less sensitivity to the force switch vs. hard cutoff for
Lennard-Jones interactions.
At the end of the day, though, the "reference" results for the CHARMM 22
force field is defined through the protocol employed to optimize the
parameters. If using the force switch leads to results demonstrably
different than *not* using the force switch, the not using the force switch
is objectively wrong. This is the stance of every single force field
developer in existence: if you use a different potential energy function
than they did, *and you get different answers*, then you are not using the
same force field. Very simple.
One of the key points from the recent CHARMM-GUI paper was to lay out the
suggested set of parameters to use with Amber to run the CHARMM force
field. Which happens to be the standard 8 A hard cutoff for
Lennard-Jones. I suggest using those until you can make use of the force
switch in Amber 16.
HTH,
Jason
--
Jason M. Swails
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Received on Wed Apr 06 2016 - 18:30:03 PDT
