Dear Amber users:
I'm confused why does the H3O+ and H2O exist electrostatic energy. The related prmtop and inpcrd (whose original prep and frcmod files were dowload from the
http://www.pharmacy.manchester.ac.uk/bryce/amber )are added to the attachment the results calculated by sander module of Amber are as follows:
H2O:
NSTEP ENERGY RMS GMAX NAME NUMBER
1 3.6676E+01 1.5945E+01 3.2183E+01 H1 2
BOND = 0.0896 ANGLE = 0.0000 DIHED = 0.0000
VDWAALS = 0.0000 EEL = 36.5866 HBOND = 0.0000
1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000
H3O+:
NSTEP ENERGY RMS GMAX NAME NUMBER
1 1.8080E+02 2.6283E+01 5.2810E+01 H2 3
BOND = 0.2262 ANGLE = 0.0000 DIHED = 0.0000
VDWAALS = 0.0000 EEL = 180.5715 HBOND = 0.0000
1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000
At the same time I have used the printBonds command to ensure the bonds are bonded to the oxgens so as the follow situations:
H2O:
Atom 1 Atom 2 R eq Frc Cnst
1 O1 ( OW) 2 H1 ( HW) 0.9570 553.0000
1 O1 ( OW) 3 H2 ( HW) 0.9570 553.0000
H3O:
Atom 1 Atom 2 R eq Frc Cnst
1 O1 ( OW) 2 H1 ( HW) 0.9570 553.0000
1 O1 ( OW) 3 H2 ( HW) 0.9570 553.0000
1 O1 ( OW) 4 H3 ( HW) 0.9570 553.0000
Now, I need you to help me to slove the doubt and thanks for your help.
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Received on Fri Apr 11 2014 - 08:00:03 PDT
