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 gmx-users@gromacs.org
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
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