Gavin Melaugh wrote:
Hi Justin
The two files processed.top and topol.top are the exact same. What is
worrying me is that when I look at the topol.tpr from gmxdump, my charge
groups do not seem to be specified the way I stated in the topology file.
Can you provide a relevant snippet of the gmxdump output to demonstrate this?
Consecutive numbering is not stated as a requirement in the manual, and if it is
in the code, then it needs to be either documented as being necessary, and/or an
enhancement request needs to be filed on redmine for non-consecutive charge
group numbering.
-Justin
Gavin
Justin A. Lemkul wrote:
Gavin Melaugh wrote:
Hi all
Do atoms belonging to the same charge group have to be indexed
consecutively in the topology file or can you have the following.
[atoms]
1 CA 1 CGE CA 1 -0.1150 12.0110
2 CB 1 CGE CB 1 0.0000 12.0110
3 CA 1 CGE CA 2 -0.1150 12.0110
4 CB 1 CGE :wq
CB 2 0.0000 12.0110
Assuming you fix this, then yes, splitting charge groups can work.
Use grompp -pp to see the post-processed topology to make sure
everything came out as expected.
-Justin
5 CA 1 CGE CA 3 -0.1150 12.0110
6 CB 1 CGE CB 3 0.0000 12.0110
7 HC 1 CGE HC 1 0.1150 1.0080
8 CU 1 CGE CU 13 0.2650 13.0190
9 NU 1 CGE NU 13 -0.5970 14.0070
10 HC 1 CGE HC 2 0.1150 1.0080
11 CU 1 CGE CU 14 0.2650 13.0190
12 NU 1 CGE NU 14 -0.5970 14.0070
13 HC 1 CGE HC 3 0.1150 1.0080
Cheers
Gavin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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