<P>
<BR>
Thanks Justin for your great help, tpbconv is working fine<BR>
Thanks once again...... <BR>
<BR>
> > it displays like this<BR>
> > Will write xtc: Compressed trajectory (portable xdr format)<BR>
> > trn version: GMX_trn_file (single precision)<BR>
> > Reading frame 0 time 1000.000<BR>
> > Setting output precision to 0.001 (nm)<BR>
> > Reading frame 1 time 1000.200 -> frame 1 time 1000.200<BR>
> > Reading frame 2 time 1000.400 -> frame 2 time 1000.400<BR>
> > Reading frame 3 time 1000.600 -> frame 3 time 1000.600<BR>
> > - -<BR>
> > - -<BR>
> > - -<BR>
> > - -<BR>
> > Reading frame 2000 time 1400.000 -> frame 2000 time 1400.000<BR>
> > Reading frame 3000 time 1600.000 -> frame 3000 time 1600.000<BR>
> > Reading frame 4000 time 1800.000 -> frame 4000 time 1800.000<BR>
> > Reading frame 5000 time 2000.000 -> frame 5000 time 2000.000<BR>
> > Reading frame 6000 time 2200.000 -> frame 6000 time 2200.000<BR>
> > -> frame 6170 time 2234.000<BR>
> ><BR>
> > gcq#85: "All Beauty Must Die" (Nick Cave)<BR>
> ><BR>
> > Any suggestions would be appreciated<BR>
><BR>
>There's no need to use trjconv; check the contents of both the .trr and .edr<BR>
>file with gmxcheck. It will output which frames are incomplete, so just choose<BR>
>a frame present in both the .trr and .edr that is complete. Then you can use<BR>
>tpbconv -time with that timepoint.<BR>
><BR>
>-Justin<BR>
><BR>
> > Thanks in advance.<BR>
> ><BR>
> > On Sat, 27 Sep 2008 Justin A.Lemkul wrote :<BR>
> > ><BR>
> > ><BR>
> > >minnale wrote:<BR>
> > >> Hi all<BR>
> > >>My system was crashed inbetween simulation, so restarted the run by<BR>
> > using tpbconv command<BR>
> > >>tpbconv -f popc.trr -e popc.edr -s popc.tpr -o popc_restart -time<BR>
> > 2235.2 -until 3000 it showing<BR>
> > >><BR>
> > >>Last frame read 6173 WARNING: Incomplete<BR>
> > frame: nr 6174 time 2234.600<BR>
> > >>-------------------------------------------------------<BR>
> > >>Program tpbconv, VERSION 3.3.1<BR>
> > >>Source code file: enxio.c, line: 401<BR>
> > >><BR>
> > >>Fatal error:<BR>
> > >>Could not find frame with time 2235.200195 in 'popc.edr'<BR>
> > >>-------------------------------------------------------<BR>
> > >><BR>
> > >>when I view the popc.edr file by using gmxcheck it showing<BR>
> > >> Opened 3nspop128new.edr as single precision energy file<BR>
> > >>frame: 500000 (index 0), t: 1000.000 Reading frame 6000 time<BR>
> > 2200.000 Last frame read 6173 WARNING:<BR>
> > Incomplete frame: nr 6174 time 2234.600<BR>
> > >>Found 6173 frames with a timestep of 0.2 ps.<BR>
> > >><BR>
> > >>its may be due in md.mdp file I am using velocites = no (I am<BR>
> > doubting because read doing restarts webpage and tpbconv -h command I<BR>
> > understood "Note that a frame with coordinates and velocities is<BR>
> > needed, which means that when you never write velocities, you can not<BR>
> > use tpbconv and you have to start the run again from the beginning"<BR>
> > ><BR>
> > >Use tpbconv -time and specify a frame that actually exists.<BR>
> > ><BR>
> > >Note that gen_vel = no is completely separate from nstvout = 0. If<BR>
> > you use gen_vel = no, it implies that the simulation is continuing from<BR>
> > a previous run. If you use nstvout = 0, you are never saving<BR>
> > velocities, and thus tpbconv will not work.<BR>
> > ><BR>
> > >-Justin<BR>
> > ><BR>
> > >><BR>
> > >>Could give me some suggestion how can I restart the crashed simulation?<BR>
> > >><BR>
> > >>Thanks alot for any suggestion.<BR>
> > >><BR>
> > >><BR>
> > >><BR>
> > >>Rediff Shopping<BR>
> > <http://adworks.rediff.com/cgi-bin/AdWorks/click.cgi/www.rediff.com/signature-default.htm/1050715198@Middle5/2206641_2199021/2201651/1?PARTNER=3&OAS_QUERY=null><BR>
> > >><BR>
> > >><BR>
> > >>------------------------------------------------------------------------<BR>
> > >><BR>
> > >>_______________________________________________<BR>
> > >>gmx-users mailing list gmx-users@gromacs.org<BR>
> > >>http://www.gromacs.org/mailman/listinfo/gmx-users<BR>
> > >>Please search the archive at http://www.gromacs.org/search before<BR>
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> > >>Can't post? Read http://www.gromacs.org/mailing_lists/users.php<BR>
> > ><BR>
> > >-- ========================================<BR>
> > ><BR>
> > >Justin A. Lemkul<BR>
> > >Graduate Research Assistant<BR>
> > >Department of Biochemistry<BR>
> > >Virginia Tech<BR>
> > >Blacksburg, VA<BR>
> > >jalemkul[at]vt.edu | (540) 231-9080<BR>
> > >http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin<BR>
> > ><BR>
> > >========================================<BR>
> ><BR>
> ><BR>
> ><BR>
> > Rediff Shopping<BR>
> > <http://adworks.rediff.com/cgi-bin/AdWorks/click.cgi/www.rediff.com/signature-default.htm/1050715198@Middle5/2206641_2199021/2201651/1?PARTNER=3&OAS_QUERY=null><BR>
> ><BR>
> ><BR>
> > ------------------------------------------------------------------------<BR>
> ><BR>
> > _______________________________________________<BR>
> > gmx-users mailing list gmx-users@gromacs.org<BR>
> > http://www.gromacs.org/mailman/listinfo/gmx-users<BR>
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> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php<BR>
><BR>
>--<BR>
>========================================<BR>
><BR>
>Justin A. Lemkul<BR>
>Graduate Research Assistant<BR>
>Department of Biochemistry<BR>
>Virginia Tech<BR>
>Blacksburg, VA<BR>
>jalemkul[at]vt.edu | (540) 231-9080<BR>
>http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin<BR>
><BR>
>========================================<BR>
><BR>
><BR>
>------------------------------<BR>
><BR>
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>End of gmx-users Digest, Vol 53, Issue 135<BR>
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