Hi,
you could use iwrap=1 to mirror the molecules leaving the original
periodic box back into that box "on the other side". Be aware, that you
then have to postprocess the trajectory properly.
Regards,
Anselm
On 02/08/13 11:26, Shobana, G . wrote:
> Hi AMBER users
> I got a problem that cropped up when i was executing my restart
> file.Im getting an error-"Bad value during floating point read"when i
> execute command.Im now in heating stage and im getting NaN values
> (**********)in my restart file.One of the molecule moves fastly from
> its position and is there any command to pull the molecule again to
> its position.This is the input file what i ve used,
>
> Stage 1 heating of nmrvii 300 to 325K
> &cntrl
> imin=0, irest=1, ntx=5,
> nstlim=10000, dt=0.0005,
> ntc=2, ntf=2,
> ntt=1, tautp=1.0,
> tempi=300.0, temp0=300.0,
> ntpr=50, ntwx=50,
> ntb=0, igb=1,
> cut=999.,rgbmax=999.
> /
>
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Received on Fri Feb 08 2013 - 04:30:02 PST
