generally you should not use a cutoff = 999 when you have a periodic system
and use PME. look at the tutorials on the amber web site. cutoff values of
around 8 or typically used for the direct space calculation.
On Tue, Oct 27, 2015 at 8:58 AM, jfliu <jfliu.itcs.ecnu.edu.cn> wrote:
> Dear Amber users,
>
> I constructed a truncated octahedral water box which has only 64
> water molecules, and I wanted to run MD simulation for these 64 water
> molecules in periodic boundary condition with cut = 999.0. But I just
> came across a problem, which reported the error like following:
>
> |Largest sphere to fit in unit cell has radius = 6.450
> | New format PARM file being parsed.
> | Version = 1.000 Date = 10/27/15 Time = 20:05:34
> NATOM = 195 NTYPES = 2 NBONH = 195 MBONA = 0
> NTHETH = 0 MTHETA = 0 NPHIH = 0 MPHIA = 0
> NHPARM = 0 NPARM = 0 NNB = 260 NRES = 65
> NBONA = 0 NTHETA = 0 NPHIA = 0 NUMBND = 2
> NUMANG = 0 NPTRA = 0 NATYP = 2 NPHB = 1
> IFBOX = 2 NMXRS = 3 IFCAP = 0 NEXTRA = 0
> NCOPY = 0
>
> SANDER BOMB in subroutine setup_grids
> Resulting cutoff is too small for your lower limit
>
> So, what should I do to solve this problem ? Thanks in advance !
>
> Best regards,
>
> Bob
>
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Received on Tue Oct 27 2015 - 06:30:03 PDT
