[gmx-users] Atomic distances problems using gmxcheck

[David van der Spoel]

yudaqi wrote:
> Hello gmx-users:
> 	When using gmxcheck to compare the bond length in .tpr files and .trr
> files, I get the following long list error:
> Distance between atoms 1 and 2 is 0.100, should be 0.010
> Distance between atoms 1 and 3 is 0.101, should be 0.010
> Distance between atoms 1 and 4 is 0.100, should be 0.010
> Distance between atoms 1 and 5 is 0.146, should be 0.022

If you look close the expected distance seems to be the square of the 
distance. Could it be you are using a GROMOS force field?

> ......
> 	I have searched the maillists in the web site of gromacs, and found the
> same problems has been issued by other users. However, I can not find
> detailed explanations about this. 
> 	So I wonder why the bond length should be of the order of 0.01 nm? 
> Thank you very much.
> YuDaqi
> 
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-- 
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se