[gmx-users] Re:Restarting problem of tpbconv
minnale
minnale_gnos at rediffmail.com
Sat Sep 27 20:16:28 CEST 2008
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/1050715198@Middle5/2206641_2199021/2201651/1?PARTNER=3&OAS_QUERY=null>
> > >>
> > >>
> > >>------------------------------------------------------------------------
> > >>
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> > >
> > >-- ========================================
> > >
> > >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/1050715198@Middle5/2206641_2199021/2201651/1?PARTNER=3&OAS_QUERY=null>
> >
> >
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>
>--
>========================================
>
>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
>
>========================================
>
>
>------------------------------
>
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>End of gmx-users Digest, Vol 53, Issue 135
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