AMBER Archive (2003)

Subject: water reordering in sander

From: Michael Trieb (Michael.Trieb_at_uibk.ac.at)
Date: Tue Jan 07 2003 - 07:43:38 CST

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