[gmx-users] Dihedral Restrain Syntax 4.6

[Johnny Lu]

I forget to mention that in the alanine dipeptide topol.top that I made, I
tried:
[ dihedral_restraints ]
  12 11 13 15 1 1 90 0 2000.0 1
#endif

but,
Program grompp, VERSION 4.6.5
Source code file: /build/buildd/gromacs-4.6.5/src/kernel/toppush.c, line:
1914

Fatal error:
Incorrect number of parameters - found 5, 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




On Thu, Aug 14, 2014 at 9:56 AM, Johnny Lu <johnny.lu128 at gmail.com> wrote:

> 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
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 601
>> 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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>
>