I think you should check as others did ex.: Optimization of the OPLS-AA Force
Field for Long Hydrocarbons J. Chem. Theory Comput., 2012, 8 (4), pp 1459–1470
On Monday, May 28, 2018, 8:23:50 PM GMT+3, Atila Petrosian
wrote:
Hi all,
I want to do md simulation of oil hydrocarbon?
Is t
University of Tennessee/Oak Ridge National Laboratory
Center for Molecular Biophysics
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
on behalf of Atila
Petrosian
Sent: Tuesday, May 29, 2018 9:29 PM
To: gmx-users
Subject: [gmx-users] md simulation of
Dear Micholas,
I have many hydrocarbons (small to large) for study, C8 - C50, .
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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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I know your mean. But there is not octane residue type in rtp file.
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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
I did what was in README for octane molecule, but:
Fatal error:
Residue 'LIG' not found in residue topology database.
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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
-
Dear Justin,
I found L-OPLS in GitHub:
https://github.com/wesbarnett/lopls
Can I use it directly for hydrocarbon such as octane?
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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
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?
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http:
for liquids use oplsaa
On Mon, May 28, 2018 at 12:23 PM, Atila Petrosian wrote:
> Hi all,
>
> I want to do md simulation of oil hydrocarbon?
>
> Is there appropriate force field for these hydrocarbons in gromacs?
>
> What I see in gromacs force fields only was related to aminoacids and
> nucleot
Hi all,
I want to do md simulation of oil hydrocarbon?
Is there appropriate force field for these hydrocarbons in gromacs?
What I see in gromacs force fields only was related to aminoacids and
nucleotides.
What is your suggestion for md simulation of oil hydrocarbon?
Best,
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Hi all,
I want to do md simulation of oil hydrocarbon?
Is there appropriate force field for these hydrocarbons in gromacs?
Is it possible with gromacs?
Best,
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