On Thu, Sep 26, 2013 at 5:00 AM, Yanyan ZHU <zhuyanzily.gmail.com> wrote:
> Dear All:
>
> In the MD simulations with AMBER, we set
> ioutfm=1( Binary NetCDF trajectory) to make the trail file (.mdcrd)
> smaller ,high precision and much fast to read and write
> ,and and able to accept a wider range of coordinate values .
>
> The input file as following:
> ######################################
> &cntrl
> imin=0,irest=1,ntx=5,ntxo=2,iotfm=1,
> nstlim=15000000,dt=0.002,
> ntc=2,ntf=2,ntb=2,
> ntp=2,taup=2.0,cut=10,
> ntpr=500,ntwx=1000,ntwr=1000,
> ntt=3,gamma_ln=2.0,temp0=300.0,tempi=300.0,
> /
> #########################################
>
> However, the obtained trajectory file can not be displayed with VMD . Can
> anyone give some suggestions how should I do to display the trajectory
> with VMD ?
>
Pick "NetCDF" format instead of "Amber coordinates" or "Amber coordinates
with box". If you name NetCDF trajectories with a ".nc" at the end, it
will automatically recognize the correct format.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Thu Sep 26 2013 - 04:00:02 PDT
