Hi everyone,
I am trying to simulate the Lipopolysaccharide molecule of 271 atoms. The
initial structure was drawn and saved in the .pdb format which stays as the
input file for the simulation (attached herewith).
However when I am trying to run minimization of the water molecules
restraining the molecule itself, it is showing me the output where some
energy values are ************ .
*Min_restraint.input*
Minimization
&cntrl
imin=1,
maxcyc=5000,
ncyc=2500,
ntb=1,
cut=10.0,
igb=0,
ntpr=500,
ntr=1,
ntwx=500,
ntwr=500,
ntwx=500,
ntx=1,
/
Hold solute fixed
100.0
RES 0
END
END
*OUTPUT looks like:*
NSTEP ENERGY RMS GMAX NAME NUMBER
1 3.3697E+09 5.9152E+08 5.8990E+10 O2 165
BOND = 159074.4906 ANGLE = 910.3529 DIHED =
110.2631
VDWAALS = ************* EEL = -42313.7223 HBOND =
0.0000
1-4 VDW = 29.5015 1-4 EEL = -709.5993 RESTRAINT =
0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
500 -5.9632E+07 2.2187E+11 2.1625E+13 O2 165
BOND = 2881.1840 ANGLE = 506.6092 DIHED =
130.4780
VDWAALS = 4325.9416 EEL = -52240.1784 HBOND =
0.0000
1-4 VDW = 146.6732 1-4 EEL = ************* RESTRAINT =
0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
1000 -1.1216E+07 7.7985E+09 7.6011E+11 O2 165
BOND = 2881.1838 ANGLE = 506.6089 DIHED =
130.4780
VDWAALS = 4325.9416 EEL = -52240.1784 HBOND =
0.0000
1-4 VDW = 146.6732 1-4 EEL = ************* RESTRAINT =
0.0000
Q1. What could be the error causing this?
Q2. How can I refine it to get a good minimized structure for the next
steps of simulations?
Any suggestions and help would be highly appreciated.
Thanks.
Regards,
M.Jones
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Received on Mon Aug 17 2015 - 04:00:03 PDT
