AMBER Archive (2009)

Subject: Re: [AMBER] High energy during minimization

From: aneesh cna (aneeshcna_at_gmail.com)
Date: Wed May 06 2009 - 00:58:00 CDT


Dear David and Bill,
 Thanks for your kind reply. I can able rectify the problem with leap and
structure is looking fine now, but still the system have high positive
energy during the simulation. I can't able to figure out the exact problem.
A part of the output file is given below. Please have a look and help me

*******************************************************************************************

      A V E R A G E S O V E R 100000 S T E P S

 NSTEP = 100000 TIME(PS) = 700.000 TEMP(K) = 299.91 PRESS =
199.9
 Etot = 26758.9414 EKtot = 13635.8590 EPtot =
13123.0823
 BOND = 1939.7948 ANGLE = 7047.8861 DIHED =
3285.9498
 1-4 NB = 1611.8557 1-4 EEL = 58661.2231 VDWAALS =
-19144.1023
 EELEC = -40279.5248 EHBOND = 0.0000 RESTRAINT =
0.0000
 EKCMT = 5957.0400 VIRIAL = 3338.8033 VOLUME =
606689.6355
                                                    Density =
0.9532
 Ewald error estimate: 0.2723E-04
**************************************************************************************************

Thanks in advance
Aneesh

On Sun, May 3, 2009 at 11:30 PM, Bill Ross <ross_at_cgl.ucsf.edu> wrote:

> > Unless you actually have three-atom or four-atom rings in your
> structure..
>
> If you look at it in xleap you will see all the bonds that leap
> knows about.
>
> Bill
>
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