[gmx-users] Fwd: PMF on dihedral using Gromacs 4.04

[Joanne Martin]

Hi Justin, thanks so much for the swift reply.
With regards to the mdp setting


> The proper setting for the "dihre" keyword is either "yes" or "no."

How to I specify which dihedral I want to restrain and the force constant
which I want to apply to it??

Regards,
Joanne

On Fri, Mar 4, 2011 at 1:09 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> Joanne Martin wrote:
>
>> Hi, I'm a trying to calculate the PMF of a dihedral using Gromacs version
>> 4.04.
>> I have read through all posts on the mailing list regarding this query,
>> and although Chris Neale did explain how to set the restraints for Gromacs
>> 3, these options are now obsolete for 4.04............ I get the following
>> error >
>>
>> Ignoring obsolete mdp entry 'domain-decomposition'
>> Replacing old mdp entry 'unconstrained-start' by 'continuation'
>> Ignoring obsolete mdp entry 'dihre_tau'
>> Ignoring obsolete mdp entry 'nstdihreout'
>> Ignoring obsolete mdp entry 'nstcheckpoint'
>> ERROR: invalid enum 'simple' for variable dihre, using 'no'
>>
>>
> The proper setting for the "dihre" keyword is either "yes" or "no."
>
>
>  I have read Chris's paper from 2008 on alanine dihedrals but again this is
>> done using Gromacs 3, and his tutorial for US in based on distance
>> restraints.
>>
>> Basically I have two conformations of a sugar ( a starting conformation
>> and an end conformation), and I want to generate a series of snapshots ie a
>> reaction coordinate, from a "pulled" MD, for use in US.
>> The pull code is only applicable to distance restraints, so how can I
>> apply a restraint to the dihedral so that it will sample all dihedrals from
>> the initial -180deg through to the end +180deg?
>>
>>
> You need to generate any intermediate structures at angles you wish to
> sample. There is no mechanism to enforce the rotation about a dihedral
> presently implemented in Gromacs.
>
>
>  I would really appreciate if someone could explain to me, where I should
>> set the restraints, as this is not clear from the manual.
>> Also once the initial configurations are generated, is the below mdp
>> option accurate for US of a dihedral >
>> (query regarding distance option should this be direction??)
>>
>
> The pull code is irrelevant here.  Please do not attempt to apply my
> tutorial to your problem (beyond basic theory), as you will probably only
> frustrate yourself by doing so.
>
> When using a dihedral restraint, an energy term corresponding to the
> restraint should be written to the .edr file.  I imagine you can plot these
> values as a function of the dihedral angle to extract the information you
> want.
>
> -Justin
>
>
>
>> ; Pull code
>> pull            = umbrella
>> pull_geometry   = *_distance_*  ; can't get PMF with direction
>>
>>
>> pull_dim        = N N Y
>> pull_start      = yes pull_ngroups      = 1
>> pull_group0     = ? pull_group1 = ?
>> pull_init1      = 0
>> pull_rate1      = 0.0
>> pull_k1         = 1000          ; kJ mol^-1 nm^-2
>> pull_nstxout    = 1000          ; every 2 ps
>> pull_nstfout    = 1000          ; every 2 ps
>>
>>
>>
>>
>> Can someone please get back to me with any suggestions you may have,
>>
>>
>> Kindest regards,
>> Joanne
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
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