Dear AMBER users,
We are using AMBER7 on an o3800. We performed a sander calculation on a
protein DNA complex using the NMROPT=1 flag without defining any
restraints. We find in the output that no water reordering will be done.
Therefore our questions:
- What is the main function of the "water reordering process" ?
- What consequences will this have on the md-calculations and what is
the connection between nmropt, PME and water reordering?
MD input file:
&cntrl
ntx=7, irest=1,
scnb=2.0, cut=9.0, scee=1.2, dielc=1.0,
ntp=1,
ntb=2, ntc=2, ntf=2, tol=0.000005,
nstlim=465000, ntt=1, temp0=300.0,
ntwr=1000, ntwx=500, ntpr=1000, ntwprt=0, ntwe=1000,
dt=0.002, nmropt=1, ipnlty=1, iwrap=1,
&end
&wt type='END' &end
END
MD output:
...........................
Begin reading energy term weight changes/NMR restraints
WEIGHT CHANGES:
** No weight changes given **
RESTRAINTS:
No valid redirection requests found
** No restraint defined **
Done reading weight changes/NMR restraints
| Reorder water Setup:
| ----- Reordering water will NOT be done
| NMROPT not equal 0
|
..................................
Thanks for any hints
Michael Trieb
Received on Tue Jan 07 2003 - 05:43:38 PST
