[gmx-users] dihedral restraints

[Andrew Ritchie]

It will depend on the force field parameters for each set of 4 atoms and
how much or little you want to allow them to fluctuate.  If you want to
allow some movement, some experimentation is required.  If you want them to
essentially not move, just chose an arbitrarily large number.  When I want
to remove essentially all dihedral movement, I typically choose ~ 1000
(kJ/mol/rad^2) and see very little movement.  When I'm doing umbrella
sampling about a dihedral, I typically use 50-70 (kJ/mol/rad^2).

On Mon, Mar 23, 2015 at 9:47 AM, Jessica Leuchter <
jessica.leuchter at gmail.com> wrote:

> To get the dihedrals to stay restrained to their original values what
> should the kfac be?
>
> On Fri, Mar 20, 2015 at 3:04 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
> >
> >
> > On 3/20/15 9:00 AM, Jessica Leuchter wrote:
> >
> >> Dear All,
> >>
> >> I would like to add dihedral restraints to 10 residues in my topology
> >> file using the newest version of gromacs.  I have done the
> >> following(see below) to my topology file. And this is the *grompp
> >> command* I am using: gmx grompp -f ions.mdp -c 1AKI_solv.gro -p
> >> topol.top -o ions.tpr. But I am getting the error message below.
> >>
> >> *topol.top file*:
> >>
> >> [ dihedral_restraints ]
> >> ;  ai       aj    ak      al        fnID    phi    dphi    kfac
> >>
> >>   1497  1499  1509  1511     9    -70.488     0       1
> >>   1499  1509  1511  1513     9    -12.561     0       1
> >>   1511  1513  1515  1518     9     95.706     0       1
> >>   1513  1515  1518  1520     9   -117.614     0       1
> >>   1518  1520  1522  1530     9   -111.163     0       1
> >>   1520  1522  1530  1532     9    -72.034     0       1
> >>   1530  1532  1534  1542     9   -108.627     0       1
> >>   1532  1534  1542  1544     9   -103.437     0       1
> >>   1542  1544  1554  1556     9    -80.981     0       1
> >>   1544  1554  1556  1558     9     46.231     0       1
> >>   1556  1558  1560  1570     9   -107.016     0       1
> >>   1558  1560  1570  1572     9     20.452     0       1
> >>   1570  1572  1574  1587     9    -82.626     0       1
> >>   1572  1574  1587  1589     9    169.300     0       1
> >>   1587  1589  1591  1608     9    -82.868     0       1
> >>   1589  1591  1608  1610     9    -47.555     0       1
> >>   1608  1610  1612  1623     9    -39.285     0       1
> >>   1610  1612  1623  1625     9    -72.644     0       1
> >>   1623  1625  1627  1642     9     -7.261     0       1
> >>   1625  1627  1642  1644     9    -51.880     0       1
> >>   1642  1644  1646  1652     9    -38.845     0       1
> >>   1644  1646  1652  1654     9    -73.856     0       1
> >>
> >>
> >> *Fatal error:*
> >> Incorrect number of parameters - found 2, expected 3 or 6 for Dih.
> Rest..
> >> For more information and tips for troubleshooting, please check the
> >> GROMACS
> >> website at http://www.gromacs.org/Documentation/Errors
> >>
> >>
> > Your restraints directive uses the wrong format.  See manual section
> > 5.7.1, which has a complete example of dihedral restraints and an
> > explanation of all the required columns.
> >
> > -Justin
> >
> > --
> > ==================================================
> >
> > Justin A. Lemkul, Ph.D.
> > Ruth L. Kirschstein NRSA Postdoctoral Fellow
> >
> > Department of Pharmaceutical Sciences
> > School of Pharmacy
> > Health Sciences Facility II, Room 629
> > University of Maryland, Baltimore
> > 20 Penn St.
> > Baltimore, MD 21201
> >
> > jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> > http://mackerell.umaryland.edu/~jalemkul
> >
> > ==================================================
> > --
> > 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.
> >
>
>
>
> --
> Jessica Leuchter
> Wake Forest University 2014
> 954.591.2222
> --
> 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.
>



-- 
-Andrew Ritchie