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
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com
==================================================
--
Gromacs Users mailing list
* Please search the archive at http://www.gromacs.org/Support
/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
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
==================================================
--
Gromacs Users mailing list
* Please search the archive at http://www.gromacs.org/Support
/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
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
==================================================
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a
mail to gmx-users-requ...@gromacs.org.
