Dear Amberists;
We have reported long range continuous MD simulations (50ns) in many of our
research communications. But we observe that some journals and reviewers
are very much critical of continuous MD simulations and asked for multiple
MD simulations.
But recently in a debate many people put different views on multiple MD
simulations and as per their view this multiple MD simulation does not
provide a great insight than continuous MD (50/100ns sampling). Some people
say in positive aspect to multiple MD saying that it covers a large
conformational space.
Majority of people agreed that if you are doing long range continuous MD
and proper post dynamics analysis thats enough to demonstrate maximum
points related to motions of a biological system.
As a continuous learner my question is to AMBER community that which one is
preferred a long range continuous MD or corresponding Multiple MD
simulation?
As there are numerous numbers of paper on continuous MD rather than a very
few multiple MD papers on aspects like conformational analysis and etc. so
which one is the best to go with.
Please put justification in support of your argument. We experience that
some journal and reviewers always point out to do multiple MD over
continuous MD simulation,but in maximum cases people accept long range
continuous MD.
Thanks & Regards;
Soumendranath Bhakat
Co-Founder Open Source Drug Design and In Silico Molecules (
www.insilicomolecule.org)
UKZN, Durban
Past: Birla Institute of Technology,Mesra, India
--
Thanks & Regards;
Soumendranath Bhakat
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Received on Wed Mar 05 2014 - 07:00:03 PST
