[gmx-users] positional restraint

[Alok]

hello david,
                  I checked using gmxdump.It really is not reporting the 
number of atoms.Thank you very much.
                                                                        
                                                                        
                        Alok jain

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:
>>
>>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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>>