It seems that the trajectory is discontinuous. The coordinates in the pdb file generated from the trajectory files show that the model corresponding to 2ns in the 2ns.pdb(at the last ) file is different from the model corresponding to 2ns in the 10ns(extended).pdb( at the first)
Sarbani On Wed, 10 Sep 2008 Justin A.Lemkul wrote : > > >sarbani chattopadhyay wrote: >> The post 2ns run had crashed. >> >>The commands were >>tpbconv -f 2ns.trr -e 2ns.edr -s 2ns.tpr -extend 10000 >> >>When it crashed ,the command given was >>tpbconv -f ext10ns.trr -s ext10ns.tpr -e ext10ns.edr -o leftrun.tpr >> > >So what you're saying then is that the coordinates that were the output from >the first part (say, 2ns.gro) do not match those you find in ext10ns.tpr? How did you make that determination? Is the trajectory discontinuous? > >-Justin > >> >>On Wed, 10 Sep 2008 Justin A.Lemkul wrote : >> > >> > >> >sarbani chattopadhyay wrote: >> >> Hi all, >> >> I had used the "tpbconv" command to give continuation run on a >> 2ns simulation. I >>had >> >>provided the previois trajectory file, energy file for this. However the >> continuation run >>had >> >>crashed due to power failure and I again had to give a rerun on it. >> >> >> > >> >I'm confused. Which part crashed? Start --> 2 ns, or the post-2ns time >> frame? >> > >> >Please provide the exact commands you gave to tpbconv. >> > >> >>Everything seems to be working well but surprisingly I find that the >> coordinates of the >>atoms >> >>at 2ns , as found at the end of the 2ns simulation and the coordinates >> of the atoms at >>2ns at >> >>the start of the continuation run are different. This means that the run >> didn't start from >>the >> >>point at which ended. >> > >> >How did you make this determination? >> > >> >-Justin >> > >> >> >> >>Can anyone suggest any reason for this? >> >>Thanks in advance >> >>Sarbani >> >> >> >> >> >> >>578x38_banner2.gif <http://adworks.rediff.com/cgi-bin/AdWorks/click.cgi/ >>www.rediff.com/signature-default.htm/ >>[EMAIL PROTECTED]/2606998_2599290/2602379/1?PARTNER=3&OAS_QUERY=null> >> >> >> >> >> >>------------------------------------------------------------------------ >> >> >> >>_______________________________________________ >> >>gmx-users mailing list gmx-users@gromacs.org >> >>http://www.gromacs.org/mailman/listinfo/gmx-users >> >>Please search the archive at http://www.gromacs.org/search before posting! >> >>Please don't post (un)subscribe requests to the list. Use the www >> interface or send it to >>[EMAIL PROTECTED] >> >>Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > >> >-- ======================================== >> > >> >Justin A. Lemkul >> >Graduate Research Assistant >> >Department of Biochemistry >> >Virginia Tech >> >Blacksburg, VA >> >jalemkul[at]vt.edu | (540) 231-9080 >> >http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> > >> >======================================== >> >> >> >>578x38_banner2.gif <http://adworks.rediff.com/cgi-bin/AdWorks/click.cgi/ www.rediff.com/signature-default.htm/ [EMAIL PROTECTED]/2606998_2599290/2602379/1?PARTNER=3&OAS_QUERY=null> >> >> >>------------------------------------------------------------------------ >> >>_______________________________________________ >>gmx-users mailing list gmx-users@gromacs.org >>http://www.gromacs.org/mailman/listinfo/gmx-users >>Please search the archive at http://www.gromacs.org/search before posting! >>Please don't post (un)subscribe requests to the list. Use the www interface >>or send it to [EMAIL PROTECTED] >>Can't post? Read http://www.gromacs.org/mailing_lists/users.php > >-- ======================================== > >Justin A. Lemkul >Graduate Research Assistant >Department of Biochemistry >Virginia Tech >Blacksburg, VA >jalemkul[at]vt.edu | (540) 231-9080 >http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > >========================================
_______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
