[gmx-users] Dihedral Restrain Syntax 4.6

[Johnny Lu]

I am sorry for not describing my question clearly.
    Below is my attempt at finding the correct syntax,
    mainly based on "Dihedral restraints in 4.5.X vs 4.6"
    from http://redmine.gromacs.org/issues/1194

In md.mdp, add:
    --------------------------------------
    ; Dihedral angle restraints: No or Yes
    dihre                    = yes
    dihre-fc                 = 100
    --------------------------------------
    However, when I adapted the file for alanine dipeptide
    and amber force field, grompp gives:
         Ignoring obsolete mdp entry 'andersen_seed'
         Ignoring obsolete mdp entry 'dihre'
         Ignoring obsolete mdp entry 'dihre-fc'
     So, these are not needed, despite
     orire-fc and disre-fc are defined in manual-4.6.6

In topol.top, right after description of the molecule, add
    ----------------------------------------------------
    [ dihedral_restraints ]
     5  11  12  13     1      0  120.0  30.0   1.0   1.0
    ----------------------------------------------------
I guess these numbers represent:
    ai, aj, ak, al, type, index,   phi, dphi, kfac?,  ???
    What is that ???

Since dihre-fc doesn't exist in version 4.6.6, I guess
    the second last 1.0 is the force constant, instead of
    the scaling factor of the force constant.

Manual of Gromacs 4.6.6 says unit of the force constant is
    kJ/mol/rad^2 in section 4.3.3

Running gmxdump -s md.tpr |grep DIHRE gives the following:
    functype[166]=DIHRES,
        phiA= 120, dphiA= 30, kfacA= 1,
        phiB= 120, dphiB= 30, kfacB= 1
    0 type=166 (DIHRES)
        4 10 11 12

Maillist suggested to set dphi to zero for a harmonic potential:
    ai   aj    ak    al  type  label  phi  dphi  kfac  power
     A    B     C     D     1      1  180     0     1      2

mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2006-December/025087.html

What should be the correct syntax to add a
    harmonic dihedral constaint,
    centered at 120 degree,
    with force constant 1000 kJ/mol/rad^2
    without time/ensemble averaging ?

Also, are there parameters similar to those for distance restraint?
    Like,
        disre
        disre-weighting
        disre-fc
        disre-tau
        nstdisreout

Thank you again.


On Thu, Aug 14, 2014 at 7:37 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 8/14/14, 6:54 AM, Johnny Lu wrote:
>
>> Hi.
>>
>> Is the following syntax in .mdp file correct?
>> ;ai, aj, ak, al, Type, index, Type', low, up1, up2, fac
>>
>> I guessed it from the description of distance restraint in the gromacs
>> 4.6.6 manual.
>>
>>
> No need to guess; that's exactly what's stated in manual section 4.3.4.
>
> -Justin
>
> --
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> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
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