Hi Justin, As I dont have velocities defined in my traj. file, please can I know if theres some possibility of including them to the traj. file
cheers, chetan ________________________________________ From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul [jalem...@vt.edu] Sent: 16 September 2010 12:35 To: Discussion list for GROMACS users Subject: Re: [gmx-users] rerun warning Poojari, Chetan wrote: > Hello Mark, > > Thank you very much for quick reply. > > I am looking for LJ and coul interactions, please can i know what can be done > to avoid these warnings if incase i want to calculate kinetic quantities... > You need velocities, and thus, a .trr file. -Justin > > cheers, > chetan > ________________________________________ > From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf > Of Mark Abraham [mark.abra...@anu.edu.au] > Sent: 16 September 2010 12:12 > To: Discussion list for GROMACS users > Subject: Re: [gmx-users] rerun warning > > ----- Original Message ----- > From: "Poojari, Chetan" <c.pooj...@fz-juelich.de> > Date: Thursday, September 16, 2010 20:04 > Subject: [gmx-users] rerun warning > To: "gmx-users@gromacs.org" <gmx-users@gromacs.org> > >> Hi, >> >> I am doing rerun to calculate LJ-SR & coul-SR >> interactions and other energy terms for energygrps defined >> in mdp file. >> >> I have constrained all bonds with lincs algorithm in mdp file. >> >> While running rerun i get following warnings........ >> >> WARNING: Some frames do not contain velocities. >> Ekin, >> temperature and pressure are incorrect, >> the virial will >> be incorrect when constraints are present. >> >> >> Please can I Know if the energy values generated are they >> incorrect........if so how can i recalculate correct energies as >> i dont have velocities in my file to use g_traj > > If you're not trying to calculate the kinds of *kinetic* quantities described > in the warning, then you don't care. Your first sentence sounds like you're > after *static* quantities. If you do want kinetic quantities, then you're in > trouble. > > Mark > > ------------------------------------------------------------------------------------------------ > ------------------------------------------------------------------------------------------------ > Forschungszentrum Juelich GmbH > 52425 Juelich > Sitz der Gesellschaft: Juelich > Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 > Vorsitzender des Aufsichtsrats: MinDirig Dr. Karl Eugen Huthmacher > Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), > Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, > Prof. Dr. Sebastian M. Schmidt > ------------------------------------------------------------------------------------------------ > ------------------------------------------------------------------------------------------------ -- ======================================== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
