Hi.
Use following if you are not doing this in vmd
open tk console of vmd and type
*package require pbctools*
*pbc box*
it will work
Regards
Kshatresh
On Tue, Mar 19, 2013 at 7:30 PM, Albert <mailmd2011.gmail.com> wrote:
> Dear:
>
> I am equilibration my system in amber. however, when I visualize the
> output .rst7 file I found that I cannot open the periodic neighboring
> box in VMD. Here is my NPT .in file:
>
> pmemd.cuda -O -p sys.prmtop -c nvt.rst7 -ref nvt.rst7 -i npt1.in -o
> npt1.out -x npt1.trj -inf npt1.info -r npt1.rst7
>
> equilibration
> &cntrl
> imin=0, irest=1, ntx=5,
> nstlim=2500000, dt=0.002,
> ntc=2, ntf=2,
> cut=9.0, ntb=2, ntp=1, taup=2.0,
> ntpr=500, ntwx=500, ntwr=5000,
> ntt=3, gamma_ln=2.0,
> temp0=300.0, iwrap=1,
> ntr=1, restraintmask=':291|:1-290.CA,C,N',
> restraint_wt=6.0
> /
>
> I also found that the command in VMD:
>
> pbc box
>
> doesn't work either...
>
> thank you very much
> best
> Albert
>
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Received on Tue Mar 19 2013 - 07:30:03 PDT
