okay, Thanks
On Fri, May 11, 2018 at 5:19 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > 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 >>>>>>>>> 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. >>>> >>>> >>> > -- > ================================================== > > 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. > -- 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.