Hi,
few of my simulations are failing at minimization. I tried the following.
1. turn SHAKE off in the second minimization step (the output below is
from the second stage)
2. increase the box size in the prmtop file as suggested in the LINMIN site
in both cases the second minimization fails at step 5,000 (the min2.in
file is below)
both attempts are still causing a very high energy and causing the
collapse of the minimization. Is there a way to trace an atom from the
number provided in the prmtop file and maybe move it slightly?
'
NSTEP ENERGY RMS GMAX NAME NUMBER
600 -2.6334E+05 9.0868E-01 2.4943E+02 P 4615
BOND = 19261.0578 ANGLE = 9584.9766 DIHED =
3790.4940
VDWAALS = 36990.9522 EEL = -328179.9617 HBOND =
0.0000
1-4 VDW = 1371.7901 1-4 EEL = -7282.8634 RESTRAINT =
1125.3571
EAMBER = -264463.5543
NSTEP ENERGY RMS GMAX NAME NUMBER
650 -2.6497E+05 1.3987E+00 4.3137E+02 P 4615
BOND = 19461.6015 ANGLE = 9361.5214 DIHED =
3770.9309
VDWAALS = 37909.2016 EEL = -330675.5453 HBOND =
0.0000
1-4 VDW = 1342.6023 1-4 EEL = -7271.2460 RESTRAINT =
1126.3808
EAMBER = -266100.9337
NSTEP ENERGY RMS GMAX NAME NUMBER
700 -1.1479E+06 5.3895E+07 1.7583E+10 H484 3118
BOND = 19526.4656 ANGLE = 9332.8359 DIHED =
3769.3717
VDWAALS = 38010.1258 EEL = -1213751.7650 HBOND =
0.0000
1-4 VDW = 1339.9560 1-4 EEL = -7270.1266 RESTRAINT =
1126.0594
EAMBER = -1149043.1366
NSTEP ENERGY RMS GMAX NAME NUMBER
750 -4.8452E+07 1.6052E+11 5.2367E+13 H2 59628
BOND = 19526.4490 ANGLE = 9332.8358 DIHED =
3769.3717
VDWAALS = 38010.1177 EEL = ************* HBOND =
0.0000
1-4 VDW = 1339.9560 1-4 EEL = -7270.1267 RESTRAINT =
1126.0594
EAMBER = *************
NSTEP ENERGY RMS GMAX NAME NUMBER
800 -4.7978E+06 1.4204E+09 4.6338E+11 H2 59628
BOND = 19526.4461 ANGLE = 9332.8358 DIHED =
3769.3717
VDWAALS = 38010.1163 EEL = -4863627.1880 HBOND =
0.0000
1-4 VDW = 1339.9560 1-4 EEL = -7270.1267 RESTRAINT =
1126.0594
EAMBER = -4798918.5887
'
min2.in
System minimization -fixed surface
&cntrl
imin = 1,
maxcyc = 10000,
ncyc = 5000,
ntf = 1,
ntc = 1,
ntb = 1,
ntr = 1,
iwrap = 1,
cut = 10
/
Hold Surface fixed
40.0
RES 1 1
END
END
min1.in
'System minimization -fixed Surface, functional groups, and Linker-DNA
&cntrl
imin = 1,
maxcyc = 1000,
ncyc = 500,
ntf = 1,
ntc = 1,
ntb = 1,
ntr = 1,
iwrap = 1,
cut = 10
/
Hold the Surface-APTMS and linker-DNA fixed
40.0
RES 1 41
END
END
i am using amber 10
$AMBERHOME/exe/sander.MPI -O -i min2.in \
-o ssDNAlnmn2.out \
-p ssDNAln.prmtop \
-c ssDNAlnmn1.rst \
-r ssDNAlnmn2.rst \
-ref ssDNAlnmn1.rst
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Received on Tue Mar 16 2010 - 11:30:02 PDT
