From: Leonardo Sepulveda Durán (leonardosepulveda_at_gmail.com)
Date: Tue Jul 05 2005 - 14:18:25 CDT
Hello
I have had troubles with a protein MD. I used the same script as
always to generate a structure with a waterbox and ions. After adding
the WB, y used
autoionize -psf wt-wb.psf -pdb wt-wb.pdb -is 0.00 -o wt-wb-ionized
to add ions and this was part of the output
Autoionize) System net charge before adding ions: -4.99999718041e
Autoionize) Adding 4 Na and 0 Cl ions, total 4 ions
Autoionize) System net charge after adding ions: -0.999997180407e
and the output of a minimization
TCL: Minimizing for 1000 steps
PRESSURE: 0 1.44572e+09 8.54374e+08 -8.59772e+08 8.54375e+08
9.39174e+09 -4.57774e+08 -8.59772e+08 -4.57773e+08 8.40889e+08
GPRESSURE: 0 1.44569e+09 8.54354e+08 -8.59688e+08 8.54238e+08
9.39191e+09 -4.57767e+08 -8.59756e+08 -4.57674e+08 8.40905e+08
ETITLE: TS BOND ANGLE DIHED
IMPRP ELECT VDW BOUNDARY MISC
KINETIC TOTAL TEMP TOTAL2
TOTAL3 TEMPAVG PRESSURE GPRESSURE
VOLUME PRESSAVG GPRESSAVG
ENERGY: 0 8580.8720 2578.2836 921.8960
1.1239 -5488.6144 99999999.9999 0.0000
0.0000 0.0000 99999999.9999 0.0000
99999999.9999 99999999.9999 0.0000 99999999.9999
99999999.9999 284073.1727 99999999.9999 99999999.9999
and then minimizes well
but the system is not neutral. To solve that problem i used other
autoionize setting:
autoionize -psf wt-wb.psf -pdb wt-wb.pdb -from 5 -between 10 -nna 6
-ncl 1 -o wt-wb-ionized
Autoionize) System net charge before adding ions: -4.99999718377e
Autoionize) Adding 6 SOD and 1 CLA residues...
Autoionize) System net charge after adding ions: 2.81623615273e-06e
after the same firt step in minimization, the program gave this
INITIAL STEP: 1e-06
GRADIENT TOLERANCE: 0
BRACKET: 0 0 -0 -0 -0
RESTARTING CONJUGATE GRADIENT ALGORITHM
INITIAL STEP: 2.5e-07
GRADIENT TOLERANCE: 0
BRACKET: 0 0 -0 -0 -0
lowering the INITIAL STEP indefinitely
the same happens if i use
autoionize -psf wt-wb.psf -pdb wt-wb.pdb -nna 6 -ncl 1 -o wt-wb-ionized
autoionize -psf wt-wb.psf -pdb wt-wb.pdb -nna 5 -ncl 0 -o wt-wb-ionized
autoionize -psf wt-wb.psf -pdb wt-wb.pdb -is 0.1 -o wt-wb-ionized
I dont know how to fix the problem. I would like to use a neutral
system. Does anyone have some idea about???
Leonardo
Universidad de Chile
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