Re: [gmx-users] How to mearg Ligand protein and Lipid
On 9/3/14, 12:46 AM, RINU KHATTRI wrote: hello justin i made tc_group for protein ligand and popc but i have merged protein_ligand_popc and sol_cl i made only two group now im running long simulation what can i do is this two tc_group can create the wrong analysis. No idea. I doubt it will lead to any severe artifacts. Technically speaking, anything other than one thermostat is incorrect but commonplace because of algorithmic problems in many thermostats. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 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] How to mearg Ligand protein and Lipid
Hello All I am trying to perform MD for protein ligand protein complex in popc lipid with charmm36 force field and also follow Justin A. Lemkul tutorial. I also wanted to ask that while create special index groups consisting of solvent + ions and protein + lipids using make_ndx if i am having a system with ligand molecule also then should I add it with protein lipid complex or add it separately with protein like 16 | 14 to merge the SOL and CL groups 1 | 13 | to merge Protein and POPC groups and 1 | 12 to merge Protein and LIGAND groups or I can add them like 1 | 12 | 13 to merge Protein and LIGAND and POPC groups With Regards Neha bharty -- 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] How to mearg Ligand protein and Lipid
On 9/2/14, 10:52 AM, neha bharti wrote: Hello All I am trying to perform MD for protein ligand protein complex in popc lipid with charmm36 force field and also follow Justin A. Lemkul tutorial. I also wanted to ask that while create special index groups consisting of solvent + ions and protein + lipids using make_ndx if i am having a system with ligand molecule also then should I add it with protein lipid complex or add it separately with protein like 16 | 14 to merge the SOL and CL groups 1 | 13 | to merge Protein and POPC groups and 1 | 12 to merge Protein and LIGAND groups or I can add them like 1 | 12 | 13 to merge Protein and LIGAND and POPC groups Yes, this is the proper way to merge three groups. I would likely create 3 tc-grps: protein+ligand, lipids, and solvent+ions. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 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] How to mearg Ligand protein and Lipid
hello justin i made tc_group for protein ligand and popc but i have merged protein_ligand_popc and sol_cl i made only two group now im running long simulation what can i do is this two tc_group can create the wrong analysis. kindly help On Wed, Sep 3, 2014 at 3:42 AM, Justin Lemkul jalem...@vt.edu wrote: On 9/2/14, 10:52 AM, neha bharti wrote: Hello All I am trying to perform MD for protein ligand protein complex in popc lipid with charmm36 force field and also follow Justin A. Lemkul tutorial. I also wanted to ask that while create special index groups consisting of solvent + ions and protein + lipids using make_ndx if i am having a system with ligand molecule also then should I add it with protein lipid complex or add it separately with protein like 16 | 14 to merge the SOL and CL groups 1 | 13 | to merge Protein and POPC groups and 1 | 12 to merge Protein and LIGAND groups or I can add them like 1 | 12 | 13 to merge Protein and LIGAND and POPC groups Yes, this is the proper way to merge three groups. I would likely create 3 tc-grps: protein+ligand, lipids, and solvent+ions. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 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.
