[AMBER] Fw:Problems with the gas energy of H3O+ and H2O

From: jinfenghuang <huangjinan00.qq.com>
Date: Fri, 11 Apr 2014 11:06:53 +0800

------------------ Original ------------------
From: "jinfenghuang";<huangjinan00.qq.com>;
Date: Thu, Apr 10, 2014 09:55 PM
To: "amber-request"<amber-request.ambermd.org>;

Subject: Problems with the gas energy of H3O+ and H2O



 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 Thu Apr 10 2014 - 20:30:02 PDT
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