RE: [AMBER] Problem with particle-mesh Ewald method

From: Ross Walker <ross.rosswalker.co.uk>
Date: Fri, 6 Mar 2009 22:10:34 -0800

Hi Yunjie,

> QMMM MD Script for Sander 9
> &cntrl
> imin=0, nstlim=10000000,
> dt=0.002,
> ntt=1, tempi=0.1, temp0=300.0,
> ntb=1,
> ntf=2, ntc=2,
> cut=9.0,
> ifqnt=1
> /
> &qmmm
> qmmask=1-12,
> qmtheory=1,
> qmcut=9.0
> /

...
...
> | Duplicated 0 dihedrals
> | Duplicated 0 dihedrals
> LOADING THE QUANTUM ATOMS AS GROUPS

I believe that it is getting stuck here because your mask is not valid. it
should probably be .1-12 for atoms 1 to 12.

Note there should also be a leading space before the &cntrl and &qmmm. I.e.
the & character should be in column 2.

All the best
Ross


/\
\/
|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
| http://www.rosswalker.co.uk | PGP Key available on request |

Note: Electronic Mail is not secure, has no guarantee of delivery, may not
be read every day, and should not be used for urgent or sensitive issues.





_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun Mar 08 2009 - 01:15:17 PST
Custom Search