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 [EMAIL PROTECTED]
> Message: 5
> Date: Wed, 19 Sep 2007 08:24:25 +0200
> From: David van der Spoel <[EMAIL PROTECTED]>
> Subject: Re: [gmx-users] Atomic distances problems using gmxcheck
> To: Discussion list for GROMACS users <[email protected]>
> Message-ID: <[EMAIL PROTECTED]>
> 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
> >
> > _______________________________________________
> > gmx-users mailing list [email protected]
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/search before posting!
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to [EMAIL PROTECTED]
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
>
_______________________________________________
gmx-users mailing list [email protected]
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
