[gmx-users] Fwd: PMF on dihedral using Gromacs 4.04
Joanne Martin
joanne.c.martin at hotmail.com
Fri Mar 4 17:07:58 CET 2011
Thanks Justin,
I think I have the restraints section sorted...........
However, once all of the dihedrals are obtained from the MDs, I would like
to do a WHAM analysis, of the reaction pathway.
As I have to run each conformation as a separate MD in order to obtain all
dihedral conformations, how can I do this.
g-wham in gmx requires .pdo files from the US output, but since I cannot use
US (in the classical sense) for a dihedral, how can i generate a final plot
of free energy vrs dihedral???
Thanks again, for all the help,
Joanne
On Fri,. Mar 4, 2011 at 1:33 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> Joanne Martin wrote:
>
>> 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??
>>
>>
> That's controlled in the topology. See the manual, section 4.3.3 and table
> 5.6.
>
> -Justin
>
> Regards,
>> Joanne
>>
>>
>> On Fri, Mar 4, 2011 at 1:09 PM, Justin A. Lemkul <jalemkul at vt.edu<mailto:
>> 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 <http://vt.edu> | (540) 231-9080
>>
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> ========================================
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>>
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>>
> --
> ========================================
>
> 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
>
> ========================================
> --
> gmx-users mailing list gmx-users at gromacs.org
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> Please search the archive at
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