Re: [gmx-users] md simulation of oil hydrocarbon

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

Re: [gmx-users] md simulation of oil hydrocarbon / L-OPLS

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

[gmx-users] md simulation of oil hydrocarbon / L-OPLS

Dear Micholas, I have many hydrocarbons (small to large) for study, C8 - C50, . -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For

Re: [gmx-users] md simulation of oil hydrocarbon / L-OPLS

...@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 such a spec

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 such a species should be straightforward to assign. -Justin --

[gmx-users] md simulation of oil hydrocarbon / L-OPLS

I know your mean. But there is not octane residue type in rtp file. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe

Re: [gmx-users] md simulation of oil hydrocarbon / L-OPLS

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

[gmx-users] md simulation of oil hydrocarbon / L-OPLS

I did what was in README for octane molecule, but: Fatal error: Residue 'LIG' not found in residue topology database. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read

Re: [gmx-users] md simulation of oil hydrocarbon / L-OPLS

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

[gmx-users] md simulation of oil hydrocarbon / L-OPLS

Dear Justin, I found L-OPLS in GitHub: https://github.com/wesbarnett/lopls Can I use it directly for hydrocarbon such as octane? -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read

Re: [gmx-users] md simulation of oil hydrocarbon / L-OPLS

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

[gmx-users] md simulation of oil hydrocarbon / L-OPLS

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? -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] md simulation of oil hydrocarbon

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 >

[gmx-users] md simulation of oil hydrocarbon

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, -- Gromacs Users

[gmx-users] md simulation of oil hydrocarbon?

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, -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before