In my opinion this is like wondering whether one should do standard MD or
free energy calculations, or explicit vs implicit solvent, or for that
matter QM vs MM. Multiple MD and long continuous MD are just two different
tools, and which one is the "right" tool depends completely on the problem
you are trying to solve, and what sort of data it requires. The best answer
is of course to do multiple very long MD, but I believe that the key to
success in this area (or any other where the tools are not fully mature) is
to recognize that compromises must often be made, and to carefully choose
the ones that have the least impact on your specific goals for the project.
For a reviewer to say that in all cases multiple short MD is better than
long MD makes no sense to me. That being said, I am very skeptical of
studies where there is no attempt to quantify precision.
carlos
On Wed, Mar 5, 2014 at 9:33 AM, Soumendranath Bhakat <
bhakatsoumendranath.gmail.com> wrote:
> 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Wed Mar 05 2014 - 07:00:04 PST
