Dear Mark, Thanks for the reply.
But one thing I am just wondering is that while calculating the RMSD, I'm considering the backbone only. So I can take the initial pdb file as reference for the trajectory. While doing so I see the RMSD graph is continuing to increase and not getting equilibrium value. Is that because my system is not minimized / equilibrated properly ? Any suggestion ? Thanks On Mon, Jul 30, 2012 at 7:33 AM, Mark Abraham <mark.abra...@anu.edu.au> wrote: > On 30/07/2012 3:39 AM, tarak karmakar wrote: >> >> Dear All, >> >> In my initial protein pdb structure I have added some external ligand >> molecules and as a result of that there are several short contacts. >> So, well, I minimized the system and then got the 'prot_min.gro' file. >> Now after the equilibration run, I plotted the RMSD of the resulting >> trajectory with respect to the initial pdb structure. So as the pdb >> had some short contacts, the resulting RMSD is showing large >> increasing value around 0.4-0.5 nm. >> >> 1) Then, is it better to plot [ for reporting purpose ] the RMSD of >> the trajectory with respect to the minimized coordinate file rather >> than w. r. t. the initial PDB file? > > > Since neither of those configurations were sampled from the target ensemble, > it's a bit hard to say they make good reference states. Doing initial MD > with position restraints on the protein stops it moving much while the > ligand gets sorted out. Use that as the reference state from which you begin > production MD. > > Better still, stop and consider how you will analyse your results before you > begin your simulation. Then you're better placed to do a simulation that > will lead to a meaningful result. > > >> 2) What is the acceptable range of RMSD for a protein simulation ? ( >> below 0.2 nm !! ) > > > It depends on a whole host of things. There's no magic number. > > Mark > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Only plain text messages are allowed! > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the www > interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Tarak -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
