Try the 'temperature' command in cpptraj.
On Fri, Nov 25, 2016 at 10:55 AM Nhai <nhai.qn.gmail.com> wrote:
>
> It you want to save a bit time, you can use pytraj (>= 1.0.9) to extract v
> and m.
>
> import pytraj as pt
> traj = pt.iterload('your.nc', top='your.parm')
> vels = [frame.velocity.copy() for frame in traj]
> mass = traj.top.mass
>
> # do something interesting here
>
> Install:
> http://amber-md.github.io/pytraj/latest/installation.html#update-to-amberhome
>
> Hai
>
>
>
> Hai Nguyen
> > On Nov 25, 2016, at 9:15 AM, diego.soler.uam.es wrote:
> >
> > Hi Gustavo,
> > Thanks for your answer.
> >
> > Yes, I've saved the velocities. Yes, I know I can do that, but the
> > format of the velocity files is quite difficult to manage (10
> > columns), and besides I would have to extract the masses from
> > somewhere else.
> >
> > I can extract the velocities of the subsystem of interest with
> > cpptraj, but the format is still the same one (not very friendly).
> >
> > It can be done, of course, but I was wondering if there's already
> > some tool implemented in AMBER allowing me do to this without having
> > to waste time writing a program to read the velocities in that
> > awful-looking format and the masses to compute the Kinetic energy.
> >
> > Thanks!
> >
> >
> > Quoting Gustavo Seabra <gustavo.seabra.gmail.com>:
> >
> >> Have you saved the velocities? AFAIK, the are not saved by default
> >> except on the restart file. Assuming you have the velocities, you
> >> can calculate the temperature by first calculating the kinetic
> >> energy, then using T=2*KE/(3*k), where k is Boltzmann constant.
> >>
> >> —
> >> Gustavo Seabra.
> >>
> >>
> >>
> >>> Em 25 de nov de 2016, à(s) 08:22, diego.soler.uam.es escreveu:
> >>>
> >>>
> >>> Hi, I 've run some simulations and I'd like to be able to extract
> >>> the instantaneous temperatures of just some of the residues. Is there
> >>> a quick way to achieve this? Like a flag with a mask or something? Or
> >>> do I have to do all the hard work processing the output files (not
> >>> much of a problem, but still, it would be nice if there was a quick
> >>> way to accomplish this)?
> >>>
> >>> Thank you
> >>>
> >>>
> >>>
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Received on Fri Nov 25 2016 - 08:00:03 PST
