[gmx-users] problem with position restraints: X0 set to zero

[Justin A. Lemkul]

Julian Garrec wrote:
> Justin A. Lemkul wrote:
>> Julian Garrec wrote:
>>  
>>> Dear GROMACS users,
>>>
>>> I am trying to equilibrate my system (monomeric protein in water) and 
>>> I want to use position restraint on heavy atoms of the solute using 
>>> the posre.itp file. For some reason, grompp applies correctly the 
>>> force constant I want, but sets all the reference positions to zero. 
>>> Of course I would like this ref. positions to be taken from my .gro 
>>> file:
>>>
>>> ${GROMPP} -debug 10 -f inp.mdp -po out.mdp -c first.gro -r first.gro 
>>> -p prm.top -o allprm.tpr -maxwarn 10
>>>
>>>
>>> Here are the first line of my posre.itp file:
>>>
>>> [ position_restraints ]
>>> ; atom  type      fx      fy      fz
>>>     1     1 567 567 567
>>>
>>>
>>> ... and the first line containing the "POSRES" flag in my tpr file 
>>> (dumped with gmxdump):
>>>
>>> functype[441]=POSRES, pos0A=( 0.00000000e+00, 0.00000000e+00, 
>>> 0.00000000e+00), fcA=( 5.67000000e+02, 5.67000000e+02, 
>>> 5.67000000e+02), pos0B=( 0.00000000e+00, 0.00000000e+00, 
>>> 0.00000000e+00), fcB=( 5.67000000e+02, 5.67000000e+02, 5.67000000e+02)
>>>
>>>
>>> Using the -debug option with grompp didn't provide me further 
>>> information.
>>>
>>> Does anybody know how to cure this problem ?
>>>
>>>     
>>
>> I don't know what pos0A is doing, but much earlier in the gmxdump 
>> output should've been something along the lines of:
>>
>> posres_xA[    0]={ 3.19200e+00,  4.72500e+00,  2.66900e+00}
>>
>> This line holds the coordinates of each of the restrained atoms.
>>
>> -Justin
>>   
> Hello Justin,
> 
> Thanks for your answer. I wanted to perform further tests before 
> answering you.
> 
> Actually, I do have such lines like:
> 
> posres_xA[    0]={ 3.19200e+00,  4.72500e+00,  2.66900e+00}
> 
> As far as I know, the lines containing the flag "functype" in the dumped 
> .tpr file define all the functions that are used to compute the 
> potential energy. Since position restraints involve additive terms of 
> the form k(x-x_0)^2, I expected that both k and x0 are defined in the 
> same "functype" line.
> 
> What I didn't say in my previous mail is that minimizing my system with 
> such restraints still induces strong deviation from the experimental 
> structure. Infact if I apply a huge force constant, I can see that the 
> restraints are properly applied. It seems that their is a strong 
> mismatching between the experimental structure and the FF I use...
> 

I can't replicate your problem.  I've done minimizations of different systems 
with different force constants for the position restraints; they always come out 
fine.

It might help to know what's in your system, how you set it up (the sequence of 
commands), what force field you're using, your .mdp file, and any other 
information you think is necessary.  Also be sure to note any error messages or 
warnings that the Gromacs tools print out for you.  They are usually quite helpful.

-Justin

> Thanks again,
> 
> Julian
> 
>>  
>>> Thanks,
>>>
>>> Julian
>>>     
>>
>>   
> 
> 

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

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

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