Hi, He's set the reference positions (in the -r file), rather than changing the initial positions (with the -c file).
Mark On Tue., 16 Jul. 2019, 19:03 ehsan shahini, <[email protected]> wrote: > Dear Salman, > > Thanks for the reply. For the first part, you are defining 5 cylinders with > a radius of 1.5. And, I'm not sure about your suggestion for editing the > .gro file in that particular manner since there is another option (function > 3,4,5) for restraining atoms in a layer. But you are changing the x and y > coordinates of the atoms. > > On Tue, 16 Jul 2019 at 19:36, Salman Zarrini <[email protected]> > wrote: > > > Hi Ehsan, > > > > Here is how I understood and would implement the flat-bottom potential; > > > > Just suppose you intend to confine a molecule with five atoms in a > cylinder > > with radius of *\rho = 1.500* nm and axes positioned at *x = 3.000 and y > = > > 3.000 nm* parallel to the Z. > > First you need a posre.rho.itp in which the restrain's properties are > > defined; > > posre.rho.itp > > ;Z - Cylinder: > > [ position_restraints ] > > ; i funct g_z \rho(nm) K(kJ mol-1 nm-2) > > 1 2 8 *1.500* 3500 > > 2 2 8 *1.500* 3500 > > 3 2 8 *1.500* 3500 > > 4 2 8 *1.500* 3500 > > 5 2 8 *1.500* 3500 > > > > Similar to all other restrains the posre.rho.itp should come in the end > of > > [moleculetype] section of the desired molecule, for instance using #ifdef > > ... #endif to be called later in mdp file. > > > > You still need one more file to be fed to grompp using -r as reference > > positions, as Mark pointed out; > > ;reference.gro > > Reference > > *127972* > > 1AMNA H14 *1* *3.000 3.000* 4.325 ;(no confinement along > > the Z) > > 1AMNA C11 *2* *3.000 3.000* 3.789 > > 1AMNA H12 *3* *3.000 3.000* 2.405 > > 1AMNA H13 *4* *3.000 3.000* 5.608 > > 1AMNA C10 *5* *3.000 3.000* 4.390 > > ... (rest of the unrestrained atoms) > > ... (rest of the unrestrained atoms) > > ... (rest of the unrestrained atoms) > > ... (rest of the unrestrained atoms) > > > > I hope it works! > > > > Cheers, > > Salman Zarrini > > > > > > On Tue, Jul 16, 2019 at 4:58 AM Mark Abraham <[email protected]> > > wrote: > > > > > Hi, > > > > > > On Tue., 16 Jul. 2019, 10:32 ehsan shahini, <[email protected]> > > > wrote: > > > > > > > Dear all, > > > > > > > > 1. I need to restrain a small molecule in a region (cylindrical) and > I > > > want > > > > to restrain all of its atoms in that region. The best tool is > > > flat-bottomed > > > > restrain but it only restrains individual atoms in their > corresponding > > > > regions and not all the atoms in a single region. > > > > > > > > Hence, if I want to change the main code related to flat-bottomed > where > > > can > > > > I find it? > > > > > > > > > > No need. Use grompp -r to restrain the position of each atom to the > same > > > position that is the centre of the desired region. > > > > > > Another question > > > > > > > > 2. Can we introduce virtual sites in Gromacs which are static and > > defined > > > > by the user via the XYZ coordinates of them? > > > > > > > > > > No, but you can have frozen particles that have whatever interactions > > that > > > you choose. > > > > > > Mark > > > > > > > > > Kind regards, > > > > > > > > Ehsan > > > > -- > > > > 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]. > > > > > -- > > 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]. > -- 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].
