Hydrocarbons with less than 200 atoms can be generate from the server I
mentioned. For larger hydrocarbons, it would be best to develop smaller
residues ( say C8 through C16 ) and stitch them together to form the larger
hydrocarbons and then validate the models/tune the parameters as necessary.
mx-us...@gromacs.org
Subject: Re: [gmx-users] md simulation of oil hydrocarbon / L-OPLS
On 5/29/18 3:08 PM, Atila Petrosian wrote:
> I know your mean. But there is not octane residue type in rtp file.
Then you'll have to make one, using the existing molecules as a guide.
The OPLS atom types for s
On 5/29/18 3:08 PM, Atila Petrosian wrote:
I know your mean. But there is not octane residue type in rtp file.
Then you'll have to make one, using the existing molecules as a guide.
The OPLS atom types for such a species should be straightforward to assign.
-Justin
--
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On 5/29/18 2:50 PM, Atila Petrosian wrote:
I did what was in README for octane molecule, but:
Fatal error:
Residue 'LIG' not found in residue topology database.
Your input coordinates use a generic name (that most model-building
programs use) that pdb2gmx doesn't recognize. Rename appropri
On 5/29/18 2:43 PM, Atila Petrosian wrote:
Dear Justin,
I found L-OPLS in GitHub:
https://github.com/wesbarnett/lopls
Can I use it directly for hydrocarbon such as octane?
I have no experience with those parameters. Test them and make sure they
reproduce what's in the paper.
-Justin
-
On 5/29/18 2:30 PM, Atila Petrosian wrote:
Hi,
I found a paper entitled " Optimization of the OPLS-AA Force Field for Long
Hydrocarbons " (https://pubs.acs.org/doi/abs/10.1021/ct200908r). They
obtained L-OPLS force field.
Which version of gromacs has L-OPLS force field?
None, you'll have t
