From: Kevin C Chan (cchan2242-c_at_my.cityu.edu.hk)
Date: Fri Nov 21 2014 - 04:20:16 CST
Thanks Axel and Josh that was very clear.
It sort of answered a question in my mind that why people rarely provide their equilibrated systems for others to continue their own simulations.
However I have one follow-up very practical question: is it valid if I extract the coor and vel of part of my equilibrium system and define the simulation box by direct assignment (cellBasisVector1,2,3) and continue with it?
Again thanks in advance,
> On 14 Nov, 2014, at 23:02, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
> On Fri, Nov 14, 2014 at 9:58 AM, Josh Vermaas <vermaas2_at_illinois.edu> wrote:
>> Not that I'm aware of, but you could use VMD to read in the coor and vel
>> files, and then only write out the subset of atoms you are interested in (I
>> think its $sel writenamdbin ...). The xsc file is a lost cause though. You
>> are shrinking your box, so you'll need to write a new one that has the
>> appropriate dimensions rather than the ones you started with.
> not to mention that this kind of change will also require proper
> equilibration, pretty much just like starting from scratch.
>> On 11/13/2014 10:49 PM, Kevin C Chan wrote:
>> Dear NAMD users,
>> I have run quite a long simulation of a complex system and I do not want to
>> "waste" it. I would like to continue the simulation with only part of my
>> previous system. Does it exist any option of “atomselect" for the NAMD
>> binaries (coor, vel, xsc) so I could use them for continuation?
>> Thanks a lot,
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
> College of Science & Technology, Temple University, Philadelphia PA, USA
> International Centre for Theoretical Physics, Trieste. Italy.
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