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 - 18:00:03 PDT
