Hello Everyone,
I am having 5ns mdcrd file and I want to minimize it further with imin=5 for
maxcyc=5000. But here I am getting the mdcrd file having only one frame and
no rst file.
The out file shows that it ran for one step, Can anyone help me with this
error? I am using Amber10.
*min.in file (minimization input file)*
&cntrl
imin = 5,
maxcyc = 5000,
ncyc = 2000,
ntb = 0,
ntr = 0,
cut = 12, ntpr = 1, ntwx = 1,
nmropt=0,
/
*Min.out file is pasted below:*
Maximum number of minimization cycles reached.
FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME NUMBER
5000 -8.7965E+04 3.1104E+00 8.1496E+01 HB2 1765
BOND = 13550.5326 ANGLE = 985.3458 DIHED =
3417.9826
VDWAALS = 27007.4725 EEL = -149685.0349 HBOND =
0.0000
1-4 VDW = 1250.1481 1-4 EEL = 15508.2819 RESTRAINT =
0.0000
minimization completed, ENE= -.87965271E+05 RMS= 0.311043E+01
minimizing coord set # 2
Frac coord min, max: -1202863.84373385 1202865.00693183
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.
SANDER BOMB in subroutine Routine: map_coords (ew_force.f)
Atom out of bounds. If a restart has been written,
restarting should resolve the error
*The command used is:* mpirun -np 4 /opt/apps/amber10/exe/sander -O -i
min.in -o LI4_min.out -p pro_LI4.top -c pro_LI4.crd -y LI4_5ns.mdcrd -r
LI4_min.crd -x LI4_min.mdcrd
--
--
SUNITA GUPTA
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Received on Fri Apr 29 2011 - 05:00:03 PDT
