Dear Sir, I finished my simulation with gromacs, but whatever orders I use to analysize the results, I always get errors. For example, when I type: g_density -f md.trr It returns:
Program g_density, VERSION 3.3.1 Source code file: gmxfio.c, line: 706 Can not open file: topol.tpr When I type: g_energy –f md.edr –o potential.xvg It returns: Program g_energy, VERSION 3.3.1 Source code file: statutil.c, line: 799 Invalid command line argument: –f When I type: g_rms –s md.tpr –f md.trr –o rmsd.xvg It returns: Program g_rms, VERSION 3.3.1 Source code file: statutil.c, line: 799 Invalid command line argument: –s When I type: g_gyrate –f md.trr –s md.tpr –o gyrate.xvg It retures: Program g_gyrate, VERSION 3.3.1 Source code file: statutil.c, line: 799 Invalid command line argument: –f I totally have no ideas about these error. I didn't get error information when I do the simulation. I should I do with this situation? Thanks! Yeping Sun CAS Key Laboratory of Pathogenic Microbiology & Immunology INSTITUTE OF MICROBIOLOGY CHINESE ACADEMY OF SCIENCES NO.1 Beichen West Road,Chaoyang District,Beijing 100101,china --- 11年12月13日，周二, Tsjerk Wassenaar <[email protected]> 写道： 发件人: Tsjerk Wassenaar <[email protected]> 主题: Re: [gmx-users] How to neutralize 0.748e system charge 收件人: "Discussion list for GROMACS users" <[email protected]> 日期: 2011年12月13日,周二,下午7:22 Hi Sundar, Just add 0.748 Cl- But you might want to go back through your workflow and the topology resulting from it, to see how you ended up with a non-integer charge. It is sort of unphysical. Cheers, Tsjerk On Tue, Dec 13, 2011 at 11:59 AM, Sundargenesan <[email protected]> wrote: > Dear GROMACS users, > > > Total charge of my system: > > Including chain 1 in system: 2041 atoms 207 residues > > Including chain 2 in system: 2036 atoms 206 residues > > Including chain 3 in system: 44 atoms 1 residues > > Now there are 4121 atoms and 414 residues > > Total mass in system 46007.483 a.m.u. > > Total charge in system 0.748 e > > > > Is it possible to make charge in system zero and how? > > > Thanks in advance for your reply > > > -- > gmx-users mailing list [email protected] > 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 [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
-- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
