[gmx-users] positional restraint

[David van der Spoel]

On Thu, 2004-11-25 at 17:28 +0530, Alok wrote:
> hello gmx uers,
>                         I have a problem concerning positional restraint 
> . I am constraining a residue from my protein during minimization and 
> consequently during the early  stage of my dynamics. I have consequently 
> constructed an ".itp file" for the purpose of positional restraint of 
> the residue which i then add to the ".top file".
> 
> The  .itp file is as shown below:
> 
> ; In this topology include file, you will find position restraint
> ; entries for all the heavy atoms in your original pdb file.
> ; This means that all the protons which were added by pdb2gmx are
> ; not restrained.
> 
> [ position_restraints ]
> ; atom  type      fx      fy      fz
>    691     1      100000  100000  100000
>    692     1      100000  100000  100000
>    693     1      100000  100000  100000
>    694     1      100000  100000  100000
>    695     1      100000  100000  100000
>    696     1      100000  100000  100000
>    697     1      100000  100000  100000
>    698     1      100000  100000  100000
>    699     1      100000  100000  100000
>    700     1      100000  100000  100000
>    701     1      100000  100000  100000
> 
> The output data that i get after preprocessing my input files for 
> minimization is as follows:
> 
> processing coordinates...
> double-checking input for internal consistency...
> Reading position restraint coords from out2sxl.gro
> renumbering atomtypes...
> converting bonded parameters...
> #      BONDS:   39330
> #   G96BONDS:   2817
> #     ANGLES:   26220
> #  G96ANGLES:   5464
> #      PDIHS:   2470
> #      IDIHS:   2285
> #       LJ14:   4581
> #     POSRES:   22
> 
> Here i observe that the POSRES: 22 value is twice the number of atoms 
>  of the residue (11 atoms) I want to constrain.
It's probably ok, because IIRC it is not printing the number of atoms.
Check by running gmxdump -s topol.tpr | less and search for POSRES
> 
> Also the values reported for the other terms like BONDS,ANGLES, etc 
> looks not to tally with the actual number present in the system.
> 
> I tried preprocessing the input files with different number of atoms in 
> the ".itp file" but everytime the POSRES value is twice the actual 
> number of atoms.
>  
> Can anyone please tell me the reason for this ???????
> 
> Also i would like to mention that if i still run the Mdrun program i get 
> the position restraint energy term in my energy list output file which 
> suggest that my constrain in functioning.Still I am confused about the 
> number of atoms reported for constraining after preprocessing.
>                                                                         
>                                                                         
>                                         Thanking you,
>                                                                         
>                                                                         
>                                              Alok jain
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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