Moltemplate data file problem

Dear all ,

I have a problem and i will be grateful if you can answer it .
I tried to make data file for an aromatic molecule with Moltemplate , after that when i want to check it by VMD and TopoTools with this code :

topo readlammpsdata Aromatic.data full

there is no problem but when i want to start doing MD simulation at the first step i see that this molecule is not like that and there is some dissociation inside of it .

Can you please let me know what the problem is ?

Regards,
Saeed.

Dear all ,

I have a problem and i will be grateful if you can answer it .
I tried to make data file for an aromatic molecule with Moltemplate , after
that when i want to check it by VMD and TopoTools with this code :

topo readlammpsdata Aromatic.data full

there is no problem but when i want to start doing MD simulation at the
first step i see that this molecule is not like that and there is some
dissociation inside of it .

Can you please let me know what the problem is ?

the main problem is that nobody can give advice on such an extremely
vague description.
nobody here has a crystal ball or is a mind reader.

axel.

Hi .
I am so sorry about that .
Actually I wanted to generate LAMMPS data file and input file with moltemplate .
I used " oplsaa_moltemplate.py " and I made LT file and after that I used moltemplate for converting it to LAMMPS data /input files !
It worked and I have data file and input file for my molecule , with using of VMD and topoTools I can visualize it .
But when i start MD simulation , the molecule has dissociation inside of it and it is obvious that my data file has problem .
This is strange because as I said i can visulaize the molecule by topotools and VMD !
When i run the code I have also warning like " net charge is not zero " !

I have attached my LT file with this Email.

Best Regards ,
Saeed.

Fluorene.lt (3.73 KB)

data.Fluorene (4.25 KB)

Hi .
I am so sorry about that .
Actually I wanted to generate LAMMPS data file and input file with
moltemplate .
I used " oplsaa_moltemplate.py " and I made LT file and after that I used
moltemplate for converting it to LAMMPS data /input files !
It worked and I have data file and input file for my molecule , with using
of VMD and topoTools I can visualize it .
But when i start MD simulation , the molecule has dissociation inside of it
and it is obvious that my data file has problem .

then you'll have to debug it.

This is strange because as I said i can visulaize the molecule by topotools
and VMD !

a visualization only shows the bonds and doesn't say anything about
incorrect parameters.

When i run the code I have also warning like " net charge is not zero " !

well, should the system be neutral or not? only you can know. there
are no charges assigned at all in your data file.

I have attached my LT file with this Email.

that is pointless.

axel.

Hi
I think I fixed the problem with your LT file, and posted the solution
today in a new thread. Look for a message with the subject:
"Moltemplate and OPLSAA: net charge is not zero". The problem was a
result of the atom-types you were using. Cheers.

Andrew