Hi, Note that I said solute, not solvent.
There are no relevant gaps after an effective NPT equilibration. The usual force fields do not permit it. "Gap" is a quite non-specific description, but the appearance of such is usually because the contents of the simulation cell look like a jigsaw piece (that obviously tessellates with itself). If you still think you have an issue, please upload some images to a file-sharing service and share us a link. Mark On Fri, Sep 1, 2017 at 10:12 AM Dilip H N <[email protected]> wrote: > Sir, > There is no any solvent that is protruding outside the box...all the > molecules are within the box itself, and still i am able to view the > gaps/empty area at some regions in the box...(which is indicating that the > box length is slightly bigger) > So how can i make sure that there are no any gaps in my box system and > hence proceed or further compress the box .. > > These gaps can affect the analysis part like during calculating rdf, cn, > hydrogen bond dynamics, etc...i hope so... Or doen't it affect... any > ideas..?? > > Thank you... > > > > <https://mailtrack.io/> Sent with Mailtrack > < > https://mailtrack.io/install?source=signature&lang=en&[email protected]&idSignature=22 > > > > On Fri, Sep 1, 2017 at 12:21 PM, Mark Abraham <[email protected]> > wrote: > > > Hi, > > > > These "gaps" are probably just what you expect with > > http://www.gromacs.org/Documentation/Terminology/ > > Periodic_Boundary_Conditions > > for > > the configuration you are viewing. For example, if the solute protrudes > out > > one side of the box, then there will be a matching gap on the other side > of > > the box, because that's what PBC means. If you want to view a > space-filled > > box, then you need to e.g. use trjconv to make it so. > > > > NPT isn't going to tolerate a region of vacuum ;-) > > > > Mark > > > > On Fri, Sep 1, 2017 at 8:32 AM Dilip H N <[email protected]> > > wrote: > > > > > Hello, > > > I am having a peptide and water mixture in a cubic box of say 2.5 2.5 > > 2.5 > > > nm. and if i view in vmd i am able to see there are empty spaces/gaps > at > > > some areas/regions (or in other words the box length is slightly > bigger), > > > so i ran the energy minimization(with em.mdp) and followed by npt > > > simulation (with npt.mdp), to know the box length by allowing it to > > > fluctuate... > > > But after npt simulation if i view the final structure/full trajectory > in > > > vmd, the box length has decreased slightly, but still i am able to see > > > there are empty spaces/gaps within the box. Is it ok with the gaps at > > some > > > areas or the molecules should be compactly arranged within the box..?? > > > > > > I am trying with the following commands:- > > > gmx insert-molecules -f abc.gro -ci def.gro -nmol xxx -o ghi.gro # > > > inserting molecules > > > gmx solvate -cp ghi.gro -cs spc216.gro -o jkl.gro -maxsol xxx # > > > solvating with water > > > gmx grompp -f em.mdp -c jkl.gro -p topol.top -o em.tpr > # > > > energy minimization > > > gmx mdrun -v -s em.tpr -deffnm em > > > gmx grompp -f npt.mdp -c em.gro -p topol.top -o npt.tpr > # > > > npt simulation > > > gmx mdrun -v -s npt.tpr -deffnm npt > > > > > > The gmx solvate command solvates with the empty spaces... and still > after > > > energy minimization and npt simulation i am able to see some gaps in > the > > > box through vmd. > > > How to get rid of these spaces inside the box.. or get the box > compressed > > > still further with whole mixture of molecules are within the box. > > > So how can i solve this issue..?? Do i need to modify anything in the > > .mdp > > > files..or any where else..?? > > > Here are the em.mdp and npt.mdp files attached... > > > > > > Any suggestions are highly appreciated .... > > > > > > Thank you... > > > > > > -- > > > With Best Regards, > > > > > > DILIP.H.N > > > Ph.D Student > > > > > > > > > > > > <https://mailtrack.io/> Sent with Mailtrack > > > < > > > https://mailtrack.io/install?source=signature&lang=en&; > > [email protected]&idSignature=22 > > > > > > > -- > > > 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 [email protected]. > > -- > > 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 [email protected]. > > > > > > -- > With Best Regards, > > DILIP.H.N > Ph.D Student > -- > 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 [email protected]. > -- 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 [email protected].
