[gmx-users] Atomic distances problems using gmxcheck

[yudaqi]

Hello David:
	Yes, you are right. the value equals to the square of the distance,
approximately. In fact, the force field I used was GROMOS96 43a1 force
field. I have also tried the other kind of force fields, such as
OPLS-AA/L all-atom force field, the same warning was reported, but the
"should be" value seemed much more reasonable.
	Thank you very much for your help!
在 2007-09-19三的 08:24 +0200，gmx-users-request at gromacs.org写道：
> Message: 5
> Date: Wed, 19 Sep 2007 08:24:25 +0200
> From: David van der Spoel <spoel at xray.bmc.uu.se>
> Subject: Re: [gmx-users] Atomic distances problems using gmxcheck
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <46F0C099.8040204 at xray.bmc.uu.se>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> 
> 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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