Dear Justin<div>Thanks for your reply. </div><div>I didnot get any fatal error. Since, the mdrun has started (mdrun -s spc_25_eq.tpr -cpi state.cpi -c spc_25_eq.pdb -o spc_25_eq.trr -e spc_25_eq.edr -g spc_25_eq.log -append yes ), it has created new state.cpi. So I now I cannot verify it. >From now, I will definetly check the .trr and .cpi before issuing the append command. </div>
<div>And I thing, does the value of - append i.e 'yes' is compulsion for appending or just -append would work? I am asking this because once I restartd mdrun as -cpi state.cpi -append, with no 'yes' value to mdrun. It then created new gro, trr and edr files. What I found here was the .trr (generated using cpi flag) file had all the frames.</div>
<div><br></div><div>Chandan</div><div><br>--<br>Chandan kumar Choudhury<br>NCL, Pune<br>INDIA<br>
<br><br><div class="gmail_quote">On Mon, Feb 8, 2010 at 5:21 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div><div></div><div class="h5"><br>
<br>
Chandan Choudhury wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hello gmxusers !!<br>
<br>
gmxcheck on #spc_25_eq.trr prints: (#spc_25_eq.trr is the renamed from #spc_25_eq.trr.1#. mdrun was stopped due to insufficient space)<br>
<br>
Checking file #spc_25_eq.trr<br>
trn version: GMX_trn_file (single precision)<br>
Reading frame 0 time 2000.000<br>
# Atoms 33885<br>
Reading frame 200 time 3000.000<br>
WARNING: Incomplete frame: nr 214 time 3070<br>
<br>
<br>
Item #frames Timestep (ps)<br>
Step 214 5<br>
Time 214 5<br>
Lambda 214 5<br>
Coords 214 5<br>
Velocities 214 5<br>
Forces 0<br>
Box 214 5<br>
<br>
on restarting the mdrun from state.cpi<br>
<br>
mdrun -s spc_25_eq.tpr -cpi state.cpi -c spc_25_eq.pdb -o spc_25_eq.trr -e spc_25_eq.edr -g spc_25_eq.log -append yes<br>
<br>
<br>
gmxcheck on spc_25_eq.trr prints:<br>
<br>
Checking file spc_25_eq.trr<br>
trn version: GMX_trn_file (single precision)<br>
Reading frame 0 time 2000.000<br>
# Atoms 33885<br>
Last frame 13 time 2065.000<br>
<br>
<br>
Item #frames Timestep (ps)<br>
Step 14 4.99999<br>
Time 14 4.99999<br>
Lambda 14 4.99999<br>
Coords 14 4.99999<br>
Velocities 14 4.99999<br>
Forces 0<br>
Box 14 4.99999<br>
<br>
It seems that the -append command didn't append. How can the appending be done. <br>
</blockquote>
<br></div></div>
What time does "state.cpi" correspond to? You can use gmxcheck for that. If you're taking up from the original time point, then you won't get continuation. Further, above, you checked "#spc_25_eq.trr" no "spc_25_eq.trr" - are you sure you've got all your file names correct? The combination of -cpi -append should work quite well, although I think there are still some issues with file sizes >2GB, but that does not appear to be the case here (you would've gotten a fatal error).<br>
<br>
-Justin<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
Chandan<br>
<br>
--<br>
Chandan kumar Choudhury<br>
NCL, Pune<br>
INDIA<br>
<br>
</blockquote>
<br></div>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
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