On 5/11/18 1:18 PM, neelam wafa wrote:
*This is the message of gmx check for both the trajectories. I*t means that
trajectory is not continuous. Am I right?
They are continuous (md_0_1.xtc ends at t=2720 ps and traj_comp.xtc
starts at the same time) and can be concatenated together. It appears
your run did continue from the checkpoint file. I have no explanation
for why the file names are not what one would expect.
-Justin
*gmx check -f md_0_1.xtc*
Checking file md_0_1.xtc
Reading frame 0 time 0.000
# Atoms 67864
Precision 0.001 (nm)
Reading frame 200 time 2000.000
Item #frames Timestep (ps)
Step 273 10
Time 273 10
Lambda 0
Coords 273 10
Velocities 0
Forces 0
Box 273 10
* gmx check -f traj_comp.xtc*
Checking file traj_comp.xtc
Reading frame 0 time 2720.000
# Atoms 67864
Precision 0.001 (nm)
Last frame 13 time 2850.000
Item #frames Timestep (ps)
Step 14 10
Time 14 10
Lambda 0
Coords 14 10
Velocities 0
Forces 0
Box 14 10
On Fri, May 11, 2018 at 5:12 PM, neelam wafa <neelam.w...@gmail.com> wrote:
The previous command was :
gmx mdrun -deffnm md_0_1
I didn't ust -cpi falg .
On Fri, May 11, 2018 at 5:01 PM, Justin Lemkul <jalem...@vt.edu> wrote:
On 5/11/18 12:52 PM, neelam wafa wrote:
I used this command:
gmx mdrun -s md_0_1.tpr -cpi md_0_1.cpt
But I think its not appending as new files are being generated with names
state.cpt, state_prev.cpt and traj_comp.xtc
while the previous files were md_0_1.cpt, md_0_1_prev.cpt and md_0_1.xtc.
Why has it happened ? I have checked log files but not able to infer a
proper answer.
The file names are contained within the .cpt file, and those are what
will be written. You haven't said what your previous command was, but the
use of -deffnm makes this much easier:
gmx mdrun -deffnm md_0_1 -cpi
You will always get clearly named files.
If its not appened, will the final trajectory .xtc obtained cover the
whole
simmulation or I ll have to combine both results?
Use gmx check.
-Justin
Regards
On Fri, May 11, 2018 at 2:49 PM, Justin Lemkul <jalem...@vt.edu> wrote:
On 5/11/18 10:42 AM, neelam wafa wrote:
Dear Sir Justin!
I have restarted the simmulation but its producing a separate log file
starting from the step where restarted. Is it normal response or there
is
some problem with my restart?
That shouldn't happen; everything should be appended unless there was
some
problem (check the .log file itself and stdout/stderr for messages).
Appending is for convenience but there is no functional requirement for
it
(I never append on the fly by personal preference, I just concatenate
later).
-Justin
Thanks in advance.
On Fri, May 11, 2018 at 12:06 PM, neelam wafa <neelam.w...@gmail.com>
wrote:
Thanks Sir Justin!
I have continued the simmulation from the last step.
Regards
On Thu, May 10, 2018 at 12:08 PM, Justin Lemkul <jalem...@vt.edu>
wrote:
On 5/10/18 7:08 AM, neelam wafa wrote:
Hi gmx users!
I am running a 5ns md simmulation of a protein with 2500000 steps.
It
crashed at 1360000 steps due to some power problem. Now I want to
continue
this simmulation. In the manual following command is given:
mdrun -s topol.tpr -cpi state.cpt
but I am confused which file is state.cpt. I have got two cpt files
md_1_0.cpt and md_1_0_prev.cpt. which one is to be used?
Look at the time stamps of the files and inspect their contents with
gmx
check. You will see an obvious difference in what they contain. Also
consult the mdrun help info, which specifically addresses your
question.
Also I did not get a md_1_0.gro file/ Is is due to incomplete
simmulation?
Yes, because that file is only produced from the last step.
Also do I need to specify -append flag or not? I am using version
5.1.5
-append has been the default option for many years. Again, see the
mdrun
help description.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry
303 Engel Hall
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Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com
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Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com
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--
==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com
==================================================
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/Mailing_Lists/GMX-Users_List before posting!
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https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
send a mail to gmx-users-requ...@gromacs.org.
--
==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com
==================================================
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