[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."
I forgot to mention, the local environment also matters.

On Mon, Mar 23, 2015 at 10:23 AM, Andrew Ritchie <drew.w.ritchie at gmail.com>
wrote:

> 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
>> >
>> > ==================================================
>> > --
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>> >
>>
>>
>>
>> --
>> Jessica Leuchter
>> Wake Forest University 2014
>> 954.591.2222
>> --
>> Gromacs Users mailing list
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>
>
>
> --
> -Andrew Ritchie
>



-- 
-Andrew Ritchie