[gmx-users] Problem with MD simulation
marlon.sidore at gmail.com
Wed Apr 19 12:53:29 CEST 2017
you forgot about periodic boundary conditions - you need to put your
trajectory through trjconv -pbc mol to make your protein whole again.
On Apr 19, 2017 12:45 PM, "Mariusz Wierzbowski" <mariuszmw at gumed.edu.pl>
> Hi, I am not sure if this is a problem. I performed md run for a
> protein(pdb code 1rep) and I am wondering when i convert file from last ns
> with gmx editconf -f md25.gro -o md25.pdb and look at the pdb, the ds DNA
> seems divied, splitted there is one half with the protein and the second
> one bellow. Is this normal or is it wrong ? Where could I have made a
> mistake, the RMSD chart for this protein after simulations looks good.
> Thanks for all suggestions.
> 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-request at gromacs.org.
More information about the gromacs.org_gmx-users