Re: [gmx-users] md simulation of oil hydrocarbon / L-OPLS
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. This in itself is a fairly massive undertaking since you would essentially be making a new force-field (similar to how protein force-fields were developed). That being said, it would be immensely useful. === Micholas Dean Smith, PhD. MRSC Post-doctoral Research Associate 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 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 (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- 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 requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] md simulation of oil hydrocarbon / L-OPLS
Since octane is not huge hydrocarbon, you could use LigParGen ( http://zarbi.chem.yale.edu/ligpargen/gmx_tutorial.html ) from Jorgensen's lab to generate an itp file for octane, which you could use as your guide to build an rtp. -Micholas === Micholas Dean Smith, PhD. MRSC Post-doctoral Research Associate University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Justin Lemkul Sent: Tuesday, May 29, 2018 3:10 PM To: gmx-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 such a species should be straightforward to assign. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- 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 requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- 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 requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
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 -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- 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 requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
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 appropriately according to what the .rtp file wants. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- 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 requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
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 -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- 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 requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
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 to create/modify force field files. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- 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 requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
