Thanks sir Justin and sir Mark On Sat, 12 May 2018 3:27 pm Mark Abraham, <mark.j.abra...@gmail.com> wrote:
> Hi, > > Or use the existing tool one has for a group of related files, called a > directory or folder ;-) It's not compulsory to do your whole thesis in the > same folder, too :-D > > Mark > > On Fri, May 11, 2018, 21:01 Justin Lemkul <jalem...@vt.edu> wrote: > > > > > > > On 5/11/18 2:11 PM, neelam wafa wrote: > > > Hi! > > > does this means that i should not have used -deffnm md_0_1 in the run > > > command? Actually I am a student and new to gromacs and have no > experties > > > in it. I think I need to read more about md run command options. > > > > Use -deffnm, it saves you typing and makes your life easier, because > > instead of relying on generic, default file names, you know exactly what > > you did and what your files hold. > > > > -Justin > > > > > Regards > > > > > > On Fri, 11 May 2018 10:57 pm Mark Abraham, <mark.j.abra...@gmail.com> > > wrote: > > > > > >> Hi, > > >> > > >> Behaviour has changed since 5.1 to make it harder for this happen, but > > if > > >> you do not call mdrun exactly the same way, older implementations of > > >> checkpointing would try to be helpful and sometimes actually not be > > >> helpful. This only happens if you try to over manage mdrun. It's best > to > > >> leave it alone to append with default file names, or use -noappend > with > > >> default filenames and get the part number added automatically. But if > > you > > >> want to change the filenames to have a part number you manage > yourself, > > you > > >> have to manage everything else too... > > >> > > >> Mark > > >> > > >> On Fri, May 11, 2018 at 7:28 PM neelam wafa <neelam.w...@gmail.com> > > wrote: > > >> > > >>> 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. > > >>> > > >> -- > > >> 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. > -- 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.