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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