[gmx-users] positional restraint
David van der Spoel
spoel at xray.bmc.uu.se
Thu Nov 25 14:44:51 CET 2004
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 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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