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 - 07:30:02 PDT
