Re: [gmx-users] Fwd: how to get .mdp files
Thanks for your help On Sat, Feb 17, 2018 at 12:44 PM, Justin Lemkul wrote: > > > On 2/16/18 9:04 PM, neelam wafa wrote: > >> -- Forwarded message -- >> From: "neelam wafa" >> Date: 17 Feb 2018 00:57 >> Subject: how to get .mdp files >> To: >> Cc: >> >> Hi >> I am new to this list. I have run the gromacs tutorial ' lysosime in >> water'. now i have to run a protein ligand simmulation. But i am confused >> about how to generate .mdp files as in tutorial they have used five .mdp >> files which are to be downloaded from bevanlab.biochem. These are >> ions.mdp, >> em.mdp, nvt.mdp, npt.mdp and md.mdp. Are the same files to be used or >> these >> have to be generated with aome software according to the protein and >> ligand. >> > > There may be differences required to properly account for different types > of systems, and certainly you will need to make changes to the nonbonded > setup if you're using a different force field. > > There's no magic to these files - they're just plain text. You could fire > up your favorite plain text editor and write them from scratch, if you > wanted. Otherwise, just modify existing files to suit your needs, again > using nothing more than a plain text editor (vim, emacs, etc). > > -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.biochem.vt.edu/people/faculty/JustinLemkul.html > > == > > > -- > 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] Fwd: how to get .mdp files
On 2/16/18 9:04 PM, neelam wafa wrote: -- Forwarded message -- From: "neelam wafa" Date: 17 Feb 2018 00:57 Subject: how to get .mdp files To: Cc: Hi I am new to this list. I have run the gromacs tutorial ' lysosime in water'. now i have to run a protein ligand simmulation. But i am confused about how to generate .mdp files as in tutorial they have used five .mdp files which are to be downloaded from bevanlab.biochem. These are ions.mdp, em.mdp, nvt.mdp, npt.mdp and md.mdp. Are the same files to be used or these have to be generated with aome software according to the protein and ligand. There may be differences required to properly account for different types of systems, and certainly you will need to make changes to the nonbonded setup if you're using a different force field. There's no magic to these files - they're just plain text. You could fire up your favorite plain text editor and write them from scratch, if you wanted. Otherwise, just modify existing files to suit your needs, again using nothing more than a plain text editor (vim, emacs, etc). -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.biochem.vt.edu/people/faculty/JustinLemkul.html == -- 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] Fwd: how to get .mdp files
mdp file is parameter file for md simulations. You need to copy if you want to use the parameters used in the tutorial. You can also change that parameter according to your use and need. On Sat, Feb 17, 2018 at 7:34 AM, neelam wafa wrote: > -- Forwarded message -- > From: "neelam wafa" > Date: 17 Feb 2018 00:57 > Subject: how to get .mdp files > To: > Cc: > > Hi > I am new to this list. I have run the gromacs tutorial ' lysosime in > water'. now i have to run a protein ligand simmulation. But i am confused > about how to generate .mdp files as in tutorial they have used five .mdp > files which are to be downloaded from bevanlab.biochem. These are ions.mdp, > em.mdp, nvt.mdp, npt.mdp and md.mdp. Are the same files to be used or these > have to be generated with aome software according to the protein and > ligand. > > Thanks in advance. > > Regards > Neelam > -- > 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.
[gmx-users] Fwd: how to get .mdp files
-- Forwarded message -- From: "neelam wafa" Date: 17 Feb 2018 00:57 Subject: how to get .mdp files To: Cc: Hi I am new to this list. I have run the gromacs tutorial ' lysosime in water'. now i have to run a protein ligand simmulation. But i am confused about how to generate .mdp files as in tutorial they have used five .mdp files which are to be downloaded from bevanlab.biochem. These are ions.mdp, em.mdp, nvt.mdp, npt.mdp and md.mdp. Are the same files to be used or these have to be generated with aome software according to the protein and ligand. Thanks in advance. Regards Neelam -- 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.
