Re: [gmx-users] the relationship between mdp file and the force field
On 4/27/15 9:01 AM, Brett wrote: Dear Justin, I have read some of the force fields original paper, but my purpose is to use MD to settle some biological issues, thus I am afraid I do not have such deep understanding what explained in the original force field papers. For Force field 6, here I mean AMBER99SB_ILDNprotein. For the MDP files, I think AMBER99SB_ILDNprotein force field, AMBER99SB protein, AMBER 99 protein, AMBER 96 protein can have the same mdp files, GROMOS96 43a1, 43a2, I don't think that's true. I know the AMBER99sb-ILDN paper gives the appropriate details for how to treat nonbonded interactions. 45a3, 53a3, 53a5,53a6,54a7 can have the same MDP files, am I right? If we GROMOS usage doesn't change, so that's correct. modified based on the on-line lysozyme tutorial, what items should we modify based on the original lysozyme mdp diles? Anything related to nonbonded interactions - rlist, rcoulomb, rvdw, vdwtype. PME is generally used nowadays for everything, so that's common. In addition, for biological research, can we definetely say GROMOS96 54a7 is better than the other versions of GROMOS96? In comparision with the GROMOS series, what is the advantages and disavantages of OPLS-AA/L all-atom force field? For biological research is way too broad. Some force fields fare better than others for disordered proteins vs. folded proteins. Biological also encompasses membranes, nucleic acids, etc. and these force fields all vary wildly in their abilities to model those systems. You need to identify similar systems and see how well different force fields have fared. Define your problem narrowly. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] the relationship between mdp file and the force field
Dear Justin, I have read some of the force fields original paper, but my purpose is to use MD to settle some biological issues, thus I am afraid I do not have such deep understanding what explained in the original force field papers. For Force field 6, here I mean AMBER99SB_ILDNprotein. For the MDP files, I think AMBER99SB_ILDNprotein force field, AMBER99SB protein, AMBER 99 protein, AMBER 96 protein can have the same mdp files, GROMOS96 43a1, 43a2, 45a3, 53a3, 53a5,53a6,54a7 can have the same MDP files, am I right? If we modified based on the on-line lysozyme tutorial, what items should we modify based on the original lysozyme mdp diles? In addition, for biological research, can we definetely say GROMOS96 54a7 is better than the other versions of GROMOS96? In comparision with the GROMOS series, what is the advantages and disavantages of OPLS-AA/L all-atom force field? I am looking forward to getting a reply from you. Best regards. Brett At 2015-04-27 19:41:17, Justin Lemkul jalem...@vt.edu wrote: On 4/26/15 10:17 PM, Brett wrote: Dear All, In the on-line Justin tutorial on lysozyme, the several mdp files are for the specific force field OPLS-AA force field. It specifically mentioned Settings, particularly nonbonded interaction settings, will be different for other force fields. Will you please introduce to me how to modify mdp files based on the difference of the force fields? For example, if I use force field 6, what should I modify based on the mdps of the lysozyme tutorial? I am looking forward to getting your reply. Force field 6 is not very precise, because the numbering in the pdb2gmx list varies between GROMACS versions. What force field (exactly) are you using? Have you read the primary literature for the force field? Settings are given in the parametrization/validation papers and that's what you should use. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] the relationship between mdp file and the force field
On 4/26/15 10:17 PM, Brett wrote: Dear All, In the on-line Justin tutorial on lysozyme, the several mdp files are for the specific force field OPLS-AA force field. It specifically mentioned Settings, particularly nonbonded interaction settings, will be different for other force fields. Will you please introduce to me how to modify mdp files based on the difference of the force fields? For example, if I use force field 6, what should I modify based on the mdps of the lysozyme tutorial? I am looking forward to getting your reply. Force field 6 is not very precise, because the numbering in the pdb2gmx list varies between GROMACS versions. What force field (exactly) are you using? Have you read the primary literature for the force field? Settings are given in the parametrization/validation papers and that's what you should use. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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.
[gmx-users] the relationship between mdp file and the force field
Dear All, In the on-line Justin tutorial on lysozyme, the several mdp files are for the specific force field OPLS-AA force field. It specifically mentioned Settings, particularly nonbonded interaction settings, will be different for other force fields. Will you please introduce to me how to modify mdp files based on the difference of the force fields? For example, if I use force field 6, what should I modify based on the mdps of the lysozyme tutorial? I am looking forward to getting your reply. Brett -- 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.
