From: Vlad Cojocaru (vlad.cojocaru_at_mpi-muenster.mpg.de)
Date: Mon Nov 30 2015 - 10:00:35 CST
Thanks Brian for you thoughts ..
Could you point me to the references you are mentioning on othe aMD
Thanks a lot
On 11/30/2015 04:48 PM, Brian Radak wrote:
> I don't believe that aMD is being actively developed at the moment.
> Although the Hamelberg paper is not the only variation in the past few
> years, so there might be interest.
> A cursory look at the paper you linked suggests that the main
> difference is in labeling and segregating "rotable" dihedral degrees
> of freedom from the others. This distinction strikes me as a bit ad
> hoc and would likely have to be made in the code specifically for
> certain molecule types (e.g. proteins). At present, only improper and
> standard dihedral terms are accumulated separately, so this might
> require semi-elaborate changes to the code (probably a separate
> accumulator for the "rotable dihedral energy and force").
> If you want to try doing this yourself, look around the source code
> for "accelMD."
> On 11/29/2015 03:53 AM, Vlad Cojocaru wrote:
>> Dear NAMD users/developers,
>> I am wondering whether there are plans to implement the new aMD
>> scheme developed by Don Hammelberg and co-workers in NAMD ?
>> Thanks for answering
>> Best wishes
>> Dr. Vlad Cojocaru
>> Computational Structural Biology Laboratory
>> Department of Cell and Developmental Biology
>> Max Planck Institute for Molecular Biomedicine
>> Röntgenstrasse 20, 48149 Münster, Germany
>> Tel: +49-251-70365-324; Fax: +49-251-70365-399
>> Email: vlad.cojocaru[at]mpi-muenster.mpg.de
>> Brian Radak
>> Theta Early Science Program Postdoctoral Appointee
>> Leadership Computing Facility
>> Argonne National Laboratory
>> 9700 South Cass Avenue
>> Building 240, 1.D.16
>> Lemont, IL 60439-4871
>> Tel: 630/252-8643
>> email: bradak_at_anl.gov
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