From: James Starlight (jmsstarlight_at_gmail.com)
Date: Wed Mar 19 2014 - 09:38:18 CDT
thanks alot for suggestion. So after re-heating all atoms of my system will
gain a new velocities distribution. Are there any possible way to continue
simulation after introduction of the ligand preventing initial conditions
of the apo-system? Alternatively Its not quite understood for me how we can
compare results of the apo and holo system simulation (e.g influence of the
ligand binding on conformation of the protein) which were initiated from
different initial conditions (in that case velocities set).
2014-03-19 16:56 GMT+04:00 Maria Bykhovskaia <mb.ucdelcaribe_at_gmail.com>:
> This might be quite challenging, because how would you determine new
> velocoties for the ligand? Chances are, the system would get unstable and
> crash. If you add a ligand in the end of the run, it's much safer to
> minimize the system again with the ligand, reheat it, and then run.
> On Wed, Mar 19, 2014 at 5:32 AM, James Starlight <jmsstarlight_at_gmail.com>wrote:
>> Dear NAMD users!
>> I wounder to know does it possible to perform simulation beginning from
>> the coordinates and velocities of the already finished simulation with the
>> introduction of the changing to the atomic contain of the system (adding
>> ligands or ions)?
>> For instance I've simulated 100ns of the apo form of my protein and then
>> add ligand to the conformation of this protein which I've obtained at the
>> end of the apo simulation. Can I run new (holo system) simulation with the
>> velocities set from the previous run defining new velocities distribution
>> only for ligand ?
>> Thanks for help,
> Maria Bykhovskaia
> Professor and Chair, Neuroscience Department
> Director, Specialized Neuroscience Research Program
> Universidad Central del Caribe
> Bayamon, Puerto Rico
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