Hi Juliette ,
If your data is more and because of that may be -append not support you.
Then these may be help you ..
mdrun -v -deffnm use different name than previous -s your tpr file
-cpi cpt
See carefully the output and check the time at which the run
start..Is the starting time
Hello all,
I am going to restart my crashed simulations, but I am not sure which
of *_prev.cpt or *.cpt to use as they contain different written
frames.
*_prev.cpt Last frame -1 time 7462.900
*.cptLast frame -1 time 7468.965
Also on the gmx site it is stated
Long story short: backup everything (since it's a backup, and hopefully
you won't need it), then use the [whatever].cpt file. You don't want to
do work twice, do you? If you use the [whatever]_prev.cpi file, you will
calculate some frames *again* that are already there.
If you use an up-to-date
Thank you. I am using
mpirun -np 8 mdrun_mpi -deffnm md -s -o -c -g -e -x -cpi md_prev.cpt
but I dont get any output and the issued command terminates in the terminal.
Do I have to remove the -o -c -g -e -x flags from the command line?
Appreciate your help,
On 13 August 2012 15:28,
On 8/13/12 3:42 PM, Juliette N. wrote:
Thank you. I am using
mpirun -np 8 mdrun_mpi -deffnm md -s -o -c -g -e -x -cpi md_prev.cpt
but I dont get any output and the issued command terminates in the terminal.
Normally error messages are rather obvious. Check your .log file carefully or
Am 13.08.2012 21:42, schrieb Juliette N.:
Thank you. I am using
mpirun -np 8 mdrun_mpi -deffnm md -s -o -c -g -e -x -cpi md_prev.cpt
I see a md_prev.cpt. If I presume correctly that this is for the
continuation of the crashed run: Why and did you read what I wrote?
but I dont get any
Yes this is to continue a crashed run, but I dont know why my runs
crash at the very beginnig of the simulation. I am using 4.5.4 so
-append should work by default. I tried a simulation from time zero
and it works as before ( mpirun -np 8 mdrun_mpi -deffnm md -s -o -c
-g -e -x ) but as soon as I
On 8/13/12 4:08 PM, Juliette N. wrote:
Yes this is to continue a crashed run, but I dont know why my runs
crash at the very beginnig of the simulation. I am using 4.5.4 so
-append should work by default. I tried a simulation from time zero
and it works as before ( mpirun -np 8 mdrun_mpi
Sorry Justin, but I dont see whats happening...
Do I have to remove mpi or -np from the line while using -cpi *.cpt ?
mdrun -deffnm md -s -o -c -g -e -x -cpi output
Thanks!
On 13 August 2012 16:10, Justin Lemkul jalem...@vt.edu wrote:
On 8/13/12 4:08 PM, Juliette N. wrote:
Yes this is
On 8/13/12 4:16 PM, Juliette N. wrote:
Sorry Justin, but I dont see whats happening...
Do I have to remove mpi or -np from the line while using -cpi *.cpt ?
No, you don't. All you should need (provided the .cpt file is valid, which it
appears to be from the gmxcheck output from before)
I am using the same line, but it crashes...Is that because my trr
files is big that it cand append the files? It was ~ 40 GB when crash
happened...
I am using 4.5.4. I tried both with and without -append.
On 13 August 2012 16:19, Justin Lemkul jalem...@vt.edu wrote:
On 8/13/12 4:16 PM,
On 8/13/12 4:34 PM, Juliette N. wrote:
I am using the same line, but it crashes...Is that because my trr
files is big that it cand append the files? It was ~ 40 GB when crash
happened...
I am using 4.5.4. I tried both with and without -append.
If it fails with and without the -append
Thanks, maybe I should re start ... :(
On 13 August 2012 16:36, Justin Lemkul jalem...@vt.edu wrote:
On 8/13/12 4:34 PM, Juliette N. wrote:
I am using the same line, but it crashes...Is that because my trr
files is big that it cand append the files? It was ~ 40 GB when crash
happened...
Hi all,
My cpt file doesnt contain any information?!!
gmxcheck -f md.cpt gives the following:
Checking file md.cpt
# Atoms 20688
Last frame -1 time 7468.965
Item#frames Timestep (ps)
Step 1
Time 1
Lambda 1
Coords 1
On 8/13/12 4:54 PM, Juliette N. wrote:
Hi all,
My cpt file doesnt contain any information?!!
Sure it does.
gmxcheck -f md.cpt gives the following:
Checking file md.cpt
# Atoms 20688
Last frame -1 time 7468.965
Item#frames Timestep (ps)
Step 1
All right, but I was expecting some more information reflecting the
last state of the system, e.g, velocities...
Thank you,
On 13 August 2012 17:04, Justin Lemkul jalem...@vt.edu wrote:
On 8/13/12 4:54 PM, Juliette N. wrote:
Hi all,
My cpt file doesnt contain any information?!!
Sure
On 8/13/12 5:10 PM, Juliette N. wrote:
All right, but I was expecting some more information reflecting the
last state of the system, e.g, velocities...
gmxcheck verifies the integrity of the file. gmxdump will produce more detailed
information, not that it's of any particular use in this
On 14/08/2012 6:08 AM, Juliette N. wrote:
Yes this is to continue a crashed run, but I dont know why my runs
crash at the very beginnig of the simulation.
You have to look at the stderr, stdout and .log file for information.
You can't solve the problem without that.
Mark
I am using
Hello gmx-users,
I ran two short simulation in series (simulation A -- simulation B). The
output *.gro file from the simulation A was used as an input file for the
simulation B. If I compare the energy value at the end of simulation A, and
t=0 at simulation B, they are different (0.1% deviation).
Hello gmx-users,
I ran two short simulation in series (simulation A -- simulation B). The
output *.gro file from the simulation A was used as an input file for the
simulation B. If I compare the energy value at the end of simulation A, and
t=0 at simulation B, they are different (0.1% deviation).
Yongchul Chung wrote:
Hello gmx-users,
I ran two short simulation in series (simulation A -- simulation B).
The output *.gro file from the simulation A was used as an input file
for the simulation B. If I compare the energy value at the end of
simulation A, and t=0 at simulation B, they
Thanks Justin for your prompt reply. I am aware of the link you provided,
but it seems they are rather hand-waving. It would be nice if I could be
directed to a source code of some sort.
Greg
On Sat, Nov 13, 2010 at 11:50 AM, Justin A. Lemkul jalem...@vt.edu wrote:
Yongchul Chung wrote:
Forgot to mention that I am using gromacs 4.0.3 with N=19200
Greg
On Sat, Nov 13, 2010 at 12:06 PM, Yongchul Chung yxc...@case.edu wrote:
Thanks Justin for your prompt reply. I am aware of the link you provided,
but it seems they are rather hand-waving. It would be nice if I could be
On 14/11/2010 4:06 AM, Yongchul Chung wrote:
Thanks Justin for your prompt reply. I am aware of the link you
provided, but it seems they are rather hand-waving. It would be nice
if I could be directed to a source code of some sort.
They're hand-waving by design of course - a normal user
Thanks, Mark.
Greg
On Sat, Nov 13, 2010 at 12:35 PM, Mark Abraham mark.abra...@anu.edu.auwrote:
On 14/11/2010 4:06 AM, Yongchul Chung wrote:
Thanks Justin for your prompt reply. I am aware of the link you provided,
but it seems they are rather hand-waving. It would be nice if I could be
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