Hello,
Now I am doing TIP5P water simulation.
Unlike TIP3P and TIP4P water simulation,
in TIP5P water simulation, make some troubles.
I have followed below procedure.
1) In xleap
source leaprc.ff99SB
loadAmberParams frcmod.tip5p
solvateBox TP5 TP5 12 0.75
saveAmberParm TP5 tip5p.prmtop tip5p.inpcrd
ð Obtain tip5p.prmtop and tip5p.inpcrd files
2) Energy minimization
mdin file
&cntrl
igb = 0,
dielc = 1.0,
ntx = 1,
irest = 0,
ntb = 1,
ntp = 0,
temp0 = 300.0,
ntf = 1,
ntc = 1,
tol = 0.0005,
cut = 8.0,
ibelly = 0,
dt = 0.002,
maxcyc = 25000,
imin = 1,
ntmin = 2,
ntpr = 1,
ntwx = 0,
ntt = 1,
ntr = 0,
/Hold the sugar fixed
5.0
RES 1
&END
&end
&ewald
nfft1 = 48, nfft2 = 48, nfft3 = 36,
order = 4, ischrgd = 0, verbose = 0, ew_type = 0,
dsum_tol = 0.00001, netfrc = 1, skinnb = 1.0,
&end
After energy minimization with above mdin file, generated mdinfo file is
very strange.
NSTEP ENERGY RMS GMAX NAME NUMBER
25000 -7.9681E+06 4.5491E+10 2.2031E+12 O 1
BOND = 230.2710 ANGLE = 0.0000 DIHED = 0.0000
VDWAALS = -171.2044 EEL = -7968132.9306 HBOND = 0.0000
1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000
RMS and GMAX values seem to diverge.
I cannot find what is the problem with above procedure.
Please help me.
Thanks in advance.
Best regards,
Hyeona Kang
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Received on Wed Mar 06 2013 - 04:00:03 PST
