Chandan Choudhury wrote:
Dear Justin
Thanks for your reply.
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.
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.
You only need to use -append. Booleans do not need "yes" to follow.
-Justin
Chandan
--
Chandan kumar Choudhury
NCL, Pune
INDIA
On Mon, Feb 8, 2010 at 5:21 PM, Justin A. Lemkul <[email protected]
<mailto:[email protected]>> wrote:
Chandan Choudhury wrote:
Hello gmxusers !!
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)
Checking file #spc_25_eq.trr
trn version: GMX_trn_file (single precision)
Reading frame 0 time 2000.000
# Atoms 33885
Reading frame 200 time 3000.000
WARNING: Incomplete frame: nr 214 time 3070
Item #frames Timestep (ps)
Step 214 5
Time 214 5
Lambda 214 5
Coords 214 5
Velocities 214 5
Forces 0
Box 214 5
on restarting the mdrun from state.cpi
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
gmxcheck on spc_25_eq.trr prints:
Checking file spc_25_eq.trr
trn version: GMX_trn_file (single precision)
Reading frame 0 time 2000.000
# Atoms 33885
Last frame 13 time 2065.000
Item #frames Timestep (ps)
Step 14 4.99999
Time 14 4.99999
Lambda 14 4.99999
Coords 14 4.99999
Velocities 14 4.99999
Forces 0
Box 14 4.99999
It seems that the -append command didn't append. How can the
appending be done.
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).
-Justin
Chandan
--
Chandan kumar Choudhury
NCL, Pune
INDIA
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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