AMBER Archive (2005)

Subject: AMBER:FAD can't be minimized.

From: zhli_2000_at_126.com
Date: Mon Apr 11 2005 - 07:48:15 CDT

Hello, all
   It seems that I have met some troubles when I
minimize FAD before MD. The input files and error
messages are as follows,respectively:

One input file

# Control section
                        &cntrl

                        ntpr = 5,

                        nscm=1

                        cut = 10.0,

                        ntb = 0,

                        maxcyc = 5000,

                        imin = 1,

                        ntr = 0,

                        ibelly = 0,

                        &end

                        &ewald

                        &end

                        --------------------------------------
 The error message

   NSTEP ENERGY RMS GMAX NAME NUMBER
   1395 -4.7911E+02 1.7187E+00 1.2483E+01
    O2 55

 BOND = 10.4893 ANGLE = 81.6121 DIHED =
32.4489
 VDWAALS = -8.5166 EEL = -71.6359 HBOND =
0.0000
 1-4 VDW = 28.1428 1-4 EEL = -551.6532 RESTRAINT =
0.0000

     .... RESTARTED DUE TO LINMIN FAILURE ...

                    FINAL RESULTS

   NSTEP ENERGY RMS GMAX NAME NUMBER
   1399 -4.6595E+02 1.7199E+00 1.2483E+01
    O2 55

 BOND = 10.4893 ANGLE = 81.6121 DIHED =
32.4489
 VDWAALS = -8.5174 EEL = -58.4694 HBOND =
0.0000
 1-4 VDW = 28.1428 1-4 EEL = -551.6532 RESTRAINT =
0.0000

     ***** REPEATED LINMIN FAILURE *****

The other input file

# Control section
                        &cntrl

                        ntpr = 5,

                        cut = 10.0,

                        ntb = 0,

                        maxcyc = 5000,

                        ncyc = 100,

                        imin = 1,

                        ntr = 0,

                        ibelly = 0,

                        &end

                        &ewald

                        &end

-----------------------------------------
The error message

   NSTEP ENERGY RMS GMAX NAME NUMBER
    220 -2.2061E+04 4.0847E+05 3.8894E+06
    O2 55

 BOND = 33.8290 ANGLE = 157.2111 DIHED =
34.1184
 VDWAALS = -9.3059 EEL = -18.4329 HBOND =
0.0000
 1-4 VDW = 28.6541 1-4 EEL = -22287.4293 RESTRAINT =
0.0000
 Frac coord min, max: -1.745293562032484E-002 1.05035201376529 The
system has extended beyond the extent of the virtual box.
 Restarting sander will recalculate
    a new virtual box with 30 Angstroms
    extra on each side, if there is a
    restart file for this configuration.
 EWALD BOMB in subroutine Routine: map_coords
(ew_force.f)
 Atom out of bounds. If a restart has been written,
 restarting should resolve the error

What can I do to deal with these problems? Thanks very
much, ahead.
                                        irene

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