Hi Neha,
FTR I disagree strongly with the conclusions of the Charmm GUI paper - it is nothing but trying to exploit fortuitous cancellation of error so I wouldn't read too much into the various settings etc that are needed there. Consider what the results might have been if they had used say POPC (which is much more tolerant of cutoff) instead of DPPC (which in the charmm force field is super sensitive to cutoff) - you'd get an entirely different set of recommended simulation conditions.
There is no reason to believe that you would not be fine using a standard hard truncation of VDW for simulating IDP with CHARMM22* in AMBER.
If you are really worried you can wait a few weeks for AMBER 16 which supports charmm force switch for VDW. If you are super paranoid you could then compare with or without the force switch - although be aware that most of the differences you sill will likely be attributable to sampling error.
You could also try FF14SB and avoid the worries.
All the best
Ross
> On Apr 6, 2016, at 17:37, 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?
>
> I look forward to your reply.
>
> --
> Regards,
> Dr. Neha S. Gandhi,
> Vice Chancellor's Research Fellow,
> Queensland University of Technology,
> 2 George Street, Brisbane, QLD 4000
> Australia
> LinkedIn
> Research Gate
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Received on Wed Apr 06 2016 - 18:00:06 PDT
