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. If its not appened, will the final trajectory .xtc obtained cover the whole simmulation or I ll have to combine both results?
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. > -- 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.