Hello all,
I found some inconsistencies between the minimization results with amber8 and amber9.
The system under study is a peptide solution in which a 21-aa peptide with end cappings is solvated by 3 Cl- ions and 5980 TIP3P waters.
The topology files were generated by 2 different force fields, ff99 and ff02pol.r1, both implemented in amber9.
Except for where the executable 'sander' came from, the other conditions were the same for all test minimizations.
All the tests were done on Itanium2.
With the following minimization options,
&cntrl
imin = 1, maxcyc = 1000,
dx0 = 0.01, drms = 0.0001,
ntpr = 10,
&end
'sander in amber8' does minimization successfully, but 'sander in amber9' fails with 'LINMIN FAILURE'.
At the end of minimizations, the mdout looks like as follows in each case.
The same behavior was seen both with ff99 and ff02pol.r1.
----------------------------
mdout by amber8/exe/sander
----------------------------
NSTEP ENERGY RMS GMAX NAME NUMBER
1000 -7.9923E+04 5.2892E-01 1.5817E+01 O 10830
BOND = 11528.3911 ANGLE = 19.3555 DIHED = 181.1588
VDWAALS = 19984.5427 EEL = -112446.2299 HBOND = 0.0000
1-4 VDW = 44.6389 1-4 EEL = 765.3724 RESTRAINT = 0.0000
Maximum number of minimization cycles reached.
----------------------------
mdout by amber9/exe/sander
----------------------------
NSTEP ENERGY RMS GMAX NAME NUMBER
30 NaN NaN 0.0000E+00 HH31 1
BOND = NaN ANGLE = NaN DIHED = NaN
VDWAALS = -398.3763 EEL = NaN HBOND = 0.0000
1-4 VDW = NaN 1-4 EEL = NaN RESTRAINT = 0.0000
.... RESTARTED DUE TO LINMIN FAILURE ...
***** REPEATED LINMIN FAILURE *****
Please let me know why the two results are totally different.
Thanks for your reply in advance.
Seongeun Yang
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Received on Wed Nov 29 2006 - 06:07:41 PST
