[gmx-users] Time correlation function computation
Dear All, How to find time correlation function of the vectors formed by Cα of a protein in molecular dynamic simulation? Thank You. -Abantika -- 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] Non-bonded energy
Hi, So, for calculating non-bonded energy, we have to consider all pair of atoms of the protein which are separated by a distance less than the cutoff distance. Please correct me if I am wrong. - Original Message - From: "Justin Lemkul" <jalem...@vt.edu> To: gmx-us...@gromacs.org Sent: Tuesday, June 7, 2016 6:50:32 AM Subject: Re: [gmx-users] Non-bonded energy On 6/6/16 9:00 AM, ABANTIKA PAL wrote: > Hi, > > I want to know which atoms are to be considered while calculating non-bonded > energy of a protein. Whether it is all pair atom or there is a particular > criteria while selecting the atoms. > The nonbonded energy of a protein would imply that any interactions within the defined cutoffs would be included. Of course, such a quantity is not physically meaningful, but that's how it's calculated. -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.
[gmx-users] Non-bonded energy
Hi, I want to know which atoms are to be considered while calculating non-bonded energy of a protein. Whether it is all pair atom or there is a particular criteria while selecting the atoms. Thanks. Abantika -- 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] Gromacs Installation
Thanks. - Original Message - From: "Justin Lemkul" <jalem...@vt.edu> To: gmx-us...@gromacs.org Sent: Tuesday, April 12, 2016 4:54:19 PM Subject: Re: [gmx-users] Gromacs Installation On 4/12/16 7:08 AM, ABANTIKA PAL wrote: > Hi, > > I have installed GROMACS 5.1.2 by performing the steps described in the > installation guide. All the steps have been executed successfully. But, no > executable of mdrun is created in the build folder. Moreover, upon executing > "which gromacs", its showing > no gromacs in > (/usr/local/gromacs/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:/home/user1/.local/bin:/home/user1/bin > Please help how to resolve the issue. > The binary is called gmx. -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.
[gmx-users] Gromacs Installation
Hi, I have installed GROMACS 5.1.2 by performing the steps described in the installation guide. All the steps have been executed successfully. But, no executable of mdrun is created in the build folder. Moreover, upon executing "which gromacs", its showing no gromacs in (/usr/local/gromacs/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:/home/user1/.local/bin:/home/user1/bin Please help how to resolve the issue. Thanks and regards Abantika -- 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.
