hello sir, there are two proteins in a water box system.i am doing martini protein cg simulation and following this tutorial http://cgmartini.nl/index.php/tutorials-general-introduction/protein at the 7 no step i have done grompp -f dynamic.mdp -c equilibration.gro -p system.top -o dynamic.tpr mdrun -deffnm dynamic -v and run for 1 micro second.from this i have got dynamic.xtc,dynamic.gro,dynamic.edr,dynamic.log,dynamic.cpt,dynamic_prev.cpt and to go for continuting of the simulation from 1 to 2 microsecond i have done grompp -f dynamic.mdp -c dynamic.gro -p system.top -o dynamic1.tpr mdrun -deffnm dynamic1 -v from the visual inspection there is not that much of difference between the two .xtc file. did i have done any wrong for the continuity of the simulation. thanking you shahee
On 6/4/18, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 6/4/18 8:57 AM, SHAHEE ISLAM wrote: >> hi, >> i am doing thr rmsd calculation of protein,by using the command >> gmx rms -n ../ndx/index-p1-0-1.ndx -s ../dynamic.tpr -f >> ../pbc.xtc/md-0-1.xtc -o rmsd-p1-0-1.xvg -tu ns (this is for first 1 >> microsecond) >> then again i have done for the next 1 micro second >> gmx rms -n ../ndx/index-p1-0-1.ndx -s ../dynamic1.tpr -f >> ../pbc.xtc/md-1-2.xtc -o rmsd-p1-1-2.xvg -tu ns (i.e from 1 to 2 >> microsecond) >> but the problem is there is no continuity between the last valu of >> rmsd-p1-0-1.xvg and last value of rmsd-p1-1-1.xvg >> >> rmsd-p1-0-1.xvg >> 0.0000000 0.0049827 >> 0.0200000 0.1721005 >> 0.0400000 0.2209484 >> 0.0600000 0.2384352 >> . >> . >> . >> >> 999.9400635 0.8320900 >> 999.9600220 0.8242129 >> 999.9800415 0.8163539 >> 1000.0000610 0.8269945 >> >> and the rmsd-p1-1-1.xvg >> 0.0000000 0.0049169 >> 0.0200000 0.1181309 >> 0.0400000 0.1274706 >> 0.0600000 0.1289782 >> . >> . >> . >> 999.9400635 0.5308270 >> 999.9600220 0.5303858 >> 999.9800415 0.5313085 >> 1000.0000610 0.5300161 > > The fact that your time values restarted suggests that the simulation > did not continue from the previous time, rather it restarted from zero > and you have essentially two separate simulations of 1 microsecond. What > does visual inspection of the trajectory tell you? > > -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. > -- 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.