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