[gmx-users] positional restraint
alokjain at iitk.ac.in
Thu Nov 25 15:26:32 CET 2004
I checked using gmxdump.It really is not reporting the
number of atoms.Thank you very much.
David van der Spoel wrote:
>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:
>>double-checking input for internal consistency...
>>Reading position restraint coords from out2sxl.gro
>>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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