Dear Amber users,
I am trying to simulate 4 large molecules (totally 14000 atoms) with 160
negative charges (balanced by Na+).
I setup the .prmtop and .inpcrd files. Plan to minimize the system energy
first in vac, then with gb, then simulate the system with gb.
However during my first minimization in vac, the totally energy keeps
positive (although decreasing). May I know if this is normal? Thanks.
Below are the last steps:
************************************************************************************************
NSTEP ENERGY RMS GMAX NAME NUMBER
4900 4.2524E+04 6.1255E-01 1.5029E+01 Na+ 13192
BOND = 3072.5966 ANGLE = 5996.4700 DIHED =
21717.1678
VDWAALS = -4816.7280 EEL = -2387.7248 HBOND =
0.0000
1-4 VDW = 9620.1746 1-4 EEL = 9321.6567 RESTRAINT =
0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
4950 4.2483E+04 5.0476E-01 1.1085E+01 Na+ 13175
BOND = 3064.7886 ANGLE = 5976.9772 DIHED =
21720.5243
VDWAALS = -4815.9956 EEL = -2408.2766 HBOND =
0.0000
1-4 VDW = 9620.5387 1-4 EEL = 9324.8584 RESTRAINT =
0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
5000 4.2580E+04 5.7094E-01 1.2015E+01 Na+ 13175
BOND = 3058.8158 ANGLE = 5958.4449 DIHED =
21725.4094
VDWAALS = -4818.3656 EEL = -2294.1242 HBOND =
0.0000
1-4 VDW = 9621.5499 1-4 EEL = 9328.4365 RESTRAINT =
0.0000
************************************************************************************************
Regards,
--
Yan Gao
Jacobs School of Engineering
University of California, San Diego
Tel: 858-952-2308
Email: Yan.Gao.2001.gmail.com
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Received on Mon Jul 26 2010 - 11:00:03 PDT
