<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;"><DIV>Dear Sir,</DIV>
<DIV> </DIV>
<DIV>I finished my simulation with gromacs, but whatever orders I use to analysize the results, I always get errors. For example, when I type: </DIV>
<DIV>g_density -f md.trr</DIV>
<DIV>It returns: </DIV>
<DIV><BR>Program g_density, VERSION 3.3.1<BR>Source code file: gmxfio.c, line: 706</DIV>
<DIV>Can not open file:<BR>topol.tpr<BR></DIV>
<DIV>When I type: <BR> g_energy –f md.edr –o potential.xvg</DIV>
<DIV>It returns: </DIV>
<DIV>Program g_energy, VERSION 3.3.1<BR>Source code file: statutil.c, line: 799</DIV>
<DIV>Invalid command line argument:<BR>–f<BR></DIV>
<DIV>When I type: g_rms –s md.tpr –f md.trr –o rmsd.xvg</DIV>
<DIV> </DIV>
<DIV>It returns: </DIV>
<DIV>Program g_rms, VERSION 3.3.1<BR>Source code file: statutil.c, line: 799</DIV>
<DIV>Invalid command line argument:<BR>–s<BR> </DIV>
<DIV>When I type: </DIV>
<DIV>g_gyrate –f md.trr –s md.tpr –o gyrate.xvg</DIV>
<DIV>It retures: </DIV>
<DIV>Program g_gyrate, VERSION 3.3.1<BR>Source code file: statutil.c, line: 799</DIV>
<DIV>Invalid command line argument:<BR>–f<BR></DIV>
<DIV>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?</DIV>
<DIV> </DIV>
<DIV>Thanks!</DIV>
<DIV>Yeping Sun<BR>CAS Key Laboratory of Pathogenic Microbiology & Immunology<BR>INSTITUTE OF MICROBIOLOGY CHINESE ACADEMY OF SCIENCES <BR>NO.1 Beichen West Road,Chaoyang District,Beijing 100101,china<BR><BR>--- <B>11年12月13日，周二, Tsjerk Wassenaar <I><tsjerkw@gmail.com></I></B> 写道：<BR></DIV>
<BLOCKQUOTE style="BORDER-LEFT: rgb(16,16,255) 2px solid; PADDING-LEFT: 5px; MARGIN-LEFT: 5px"><BR>发件人: Tsjerk Wassenaar <tsjerkw@gmail.com><BR>主题: Re: [gmx-users] How to neutralize 0.748e system charge<BR>收件人: "Discussion list for GROMACS users" <gmx-users@gromacs.org><BR>日期: 2011年12月13日,周二,下午7:22<BR><BR>
<DIV class=plainMail>Hi Sundar,<BR><BR>Just add 0.748 Cl-<BR><BR>But you might want to go back through your workflow and the topology<BR>resulting from it, to see how you ended up with a non-integer charge.<BR>It is sort of unphysical.<BR><BR>Cheers,<BR><BR>Tsjerk<BR><BR>On Tue, Dec 13, 2011 at 11:59 AM, Sundargenesan <<A href="http://cn.mc156.mail.yahoo.com/mc/compose?to=sundargenesan@gmail.com" ymailto="mailto:sundargenesan@gmail.com">sundargenesan@gmail.com</A>> wrote:<BR>> Dear GROMACS users,<BR>><BR>><BR>> Total charge of my system:<BR>><BR>> Including chain 1 in system: 2041 atoms 207 residues<BR>><BR>> Including chain 2 in system: 2036 atoms 206 residues<BR>><BR>> Including chain 3 in system: 44 atoms 1 residues<BR>><BR>> Now there are 4121 atoms and 414 residues<BR>><BR>> Total mass in system 46007.483 a.m.u.<BR>><BR>> Total charge in system 0.748 e<BR>><BR>><BR>><BR>> Is it
possible to make charge in system zero and how?<BR>><BR>><BR>> Thanks in advance for your reply<BR>><BR>><BR>> --<BR>> gmx-users mailing list <A href="http://cn.mc156.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org" ymailto="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A><BR>> <A href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target=_blank>http://lists.gromacs.org/mailman/listinfo/gmx-users</A><BR>> Please search the archive at<BR>> <A href="http://www.gromacs.org/Support/Mailing_Lists/Search" target=_blank>http://www.gromacs.org/Support/Mailing_Lists/Search</A> before posting!<BR>> Please don't post (un)subscribe requests to the list. Use the<BR>> www interface or send it to <A href="http://cn.mc156.mail.yahoo.com/mc/compose?to=gmx-users-request@gromacs.org" ymailto="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</A>.<BR>> Can't post? Read <A
href="http://www.gromacs.org/Support/Mailing_Lists" target=_blank>http://www.gromacs.org/Support/Mailing_Lists</A><BR><BR><BR><BR>-- <BR>Tsjerk A. Wassenaar, Ph.D.<BR><BR>post-doctoral researcher<BR>Molecular Dynamics Group<BR>* Groningen Institute for Biomolecular Research and Biotechnology<BR>* Zernike Institute for Advanced Materials<BR>University of Groningen<BR>The Netherlands<BR>--<BR>gmx-users mailing list <A href="http://cn.mc156.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org" ymailto="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A><BR><A href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target=_blank>http://lists.gromacs.org/mailman/listinfo/gmx-users</A><BR>Please search the archive at <A href="http://www.gromacs.org/Support/Mailing_Lists/Search" target=_blank>http://www.gromacs.org/Support/Mailing_Lists/Search</A> before posting!<BR>Please don't post (un)subscribe requests to the list. Use the<BR>www
interface or send it to <A href="http://cn.mc156.mail.yahoo.com/mc/compose?to=gmx-users-request@gromacs.org" ymailto="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</A>.<BR>Can't post? Read <A href="http://www.gromacs.org/Support/Mailing_Lists" target=_blank>http://www.gromacs.org/Support/Mailing_Lists</A><BR></DIV></BLOCKQUOTE></td></tr></table>