[gmx-users] Result difference between Gromacs and other pakages, is it a bugs??

David spoel at xray.bmc.uu.se
Wed Jun 11 19:45:01 CEST 2003

On Wed, 2003-06-11 at 17:59, PeiQuan Chen wrote:
> Dear gmx-users:
> >use mdrun -c confout.g96 to be sure 
>     Now I use mdrun -c confout.g96 to get the coordinate files. And I use the gopenmol to measure the 
> bood distance of C-Cl. Now that I get four C-H values are 1.0900,and four H-C-H 109.471219.
>     But the energy is the same as before. I don't think the gromacs calculate the energy of the confout.g96
> conformation. Because the C-H values is 1.0900, the bond energy should be zero(Eb=Kb(L-L0)^2 ).
>     I think the gromacs caluclate the energy of the confout.gro conformation, so the bond energy is not zero.
can you check the energies in the .edr file? maybe mdrun does not write
out the last energy to the log file. How about the force? Is that zero?
> Sincerely yours
> ---- 
> PeiQuan Chen
> ________________________________________________________________________
> PeiQuan Chen 	Department of Chemistry, Nankai University
> WeiJin Road 94, TianJin, 300071, P.R.China
> phone:	(86)2223506728		Mobile Phone: (+86)13920675030
> gromacs at 163.com	
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Groeten, David.
Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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