[gmx-users] restraints definition in mdp

[Justin Lemkul]

On 5/4/16 6:12 AM, Sana Saeed wrote:
> but i didnt specified force constant for distance ..is that fine? see my topology file contents following:
>

Sorry; misread "distance" as "dihedral." Yes, there are .mdp options for 
distance restraints.

http://manual.gromacs.org/documentation/5.1.2/user-guide/mdp-options.html#nmr-refinement

The weighting factor is multiplied by disre-fc, which defaults to 1000.

-Justin

> [ intermolecular-interactions ]
> [ distance_restraints ]
> ;  i    j type label      funct        lo        up1        up2    weight
> 768  2131 1    0          1  0.640512  0.840512    1.84051          1
>
> [ angle_restraints ]
> ;  ai    aj    ak    al  type    thA      fcA    multA  thB      fcB    multB
> 770  768    2131  768  1      43.420    0.0  1      43.420  41.840    1
> 768  2131  2125  2131 1    114.89    0.0  1      114.89  41.840    1
>
> [ dihedral_restraints ]
> ;  ai    aj    ak    al  type    phiA    dphiA  fcA    phiB      dphiB  fcB
> 782  770  768  2131  1      -152.840  0.0  0.0    -152.840    0.0  41.840
> 770  768  2131  2125  1      -46.638  0.0  0.0    -46.638    0.0  41.840
> 768  2131  2125  2132  1      -42.465  0.0  0.0    -42.465    0.0  41.840
>
>
>  Sana Saeed Khan,
> Research Assistant
> Chemoinformatics Lab
> Graduate Student, MS bioinfo
> Department of Bioinformatics
> Soongsil University, Seoul, South Korea.
>
>
>
> On Wednesday, May 4, 2016 7:04 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 5/4/16 4:08 AM, Sana Saeed wrote:
>> hi gromacs experts
>> i have applied distance, angle and dihedral restraints to my ligand in a protein's pocket so that it doesnt roam around when i turn off all interactions during simulation. do i need to mention about these restraints in the mdp file? i am using gromacs 5.0 and 5.1. i have used intermolecular_interactions directive for defining these restraints.
>
> There is nothing in the .mdp file related to these.
>
>> MY SECOND QUESTION is that the force constant i used is 41.840 kj/mol/K for angle and dihedral restr. does that mean that the Force constant for distance restraint is also 41.840? as i am calculating free energy of restraints (part of absolute binding F.E) so i need force constant for distance also.
>>
>
> The force constant can be whatever you want it to be.
>
> -Justin
>
>
>> [ intermolecular-interactions ]
>> [ distance_restraints ]
>> ;   i     j type label      funct         lo        up1        up2     weight
>>   768  2131 1     0          1   0.640512   0.840512    1.84051          1
>>
>> [ angle_restraints ]
>> ;   ai    aj    ak    al  type    thA      fcA    multA  thB      fcB    multB
>>    770   768    2131  768  1      43.420    0.0   1      43.420   41.840    1
>>    768   2131   2125  2131 1     114.89    0.0   1      114.89   41.840    1
>>
>> [ dihedral_restraints ]
>> ;   ai    aj    ak    al  type    phiA     dphiA  fcA    phiB      dphiB  fcB
>>   782  770   768   2131  1       -152.840  0.0  0.0    -152.840    0.0  41.840
>>   770  768   2131  2125  1       -46.638  0.0  0.0     -46.638     0.0  41.840
>>   768  2131  2125  2132  1       -42.465   0.0  0.0    -42.465     0.0  41.840
>>
>>
>> Sana Saeed Khan,
>> Research Assistant
>> Chemoinformatics Lab
>> Graduate Student, MS bioinfo
>> Department of Bioinformatics
>> Soongsil University, Seoul, South Korea.
>>
>

-- 
==================================================

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

==================================================