Hi, On Tue, Jan 2, 2018 at 3:02 AM Seketoulie Keretsu <sekekere...@gmail.com> wrote:
> Dear Experts > > I am currently doing the gromacs tutorial for simulation of membrane > protein (KALP15 in DPPC by Justin A. Lemkul). I came across several > challenges most of which I could resolve. However, the result after > solvation wasn't as expected. That is, a small portion of the DPPC > bilayer was out of the solvation box and also the the water was no > distributed over the system as mentioned in tutorial (or atleast it > wasn't observable in VMD). I have done just as in the tutorial. I have > no clue why the bilayer went outside the solvation box since i > followed and executed just as mentioned in the tutorial. This just seems like normal consequences of a simulation using periodic boundary conditions that are then visualized without considering those consequences... see http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions > I suspect the > later issue, that is, the distribution of water all over the system > could be due to the step in which the changing of the value of C from > 0.15 to 0.375 in vdwradii.dat wasn't effective. > Why do you think that? Did you compare with leaving the value unmodified? > My questions are: > > 1. Are the other membrane protein simulation tutorials available. > Perhaps more comprehensive ones? > Justin's tutorials are of very high quality and rather comprehensive. > 2. After changing the value of C to 0.375 in the vdwradii.dat file at > the working directory, should i copy the vdwradii.dat to > /home/..../gromacs/top directory (where the file was originally > located)? > You should do whatever the tutorial suggests. In practice, both work the same. Being able to leave the modified file in the working directory is convenient in multiple ways. > 3. The tutorial mentioned " Placing the new gromos53a6_lipid.ff > directory in $GMXLIB will allow you to use this force field > system-wide." I am unable to locate 'GMXLIB'. Does GMXLIB refer to the > directory in which the forcefield files (eg. ffnonbonded.ipt) were > located or should i create a GMXLIB directory. > GMXLIB is an environment variable that is set up when you run "source /path/to/GMXRC" that helps the tools find the databases in /path/to/gromacs/share/top. You could put the directory there, or leave it in your working directory, whatever is more useful and convenient for you. Do you plan to use it again? Mark > The problems seems trivial however I am unable to proceed beyond > solvation. Kindly give suggestions. > > Thank you. > > > Sincerely, > Seke > -- > 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.