[gmx-users] cutting off the backbone bonds in polymer

[hjqian at jlu.edu.cn]

Dear All,

I am simulating a polystyrene melt with OPLS-AA force field.  At the moment I am trying to cut off the bonds connecting styrene units on the chain backbone. Consequently, all the bond angles and dihedrals crossing these removed backbone bonds are also deleteted from the *.top file. However, in order to make a fair comparison of the LJ energy with original polystyrene melt. I would like to keep the interaction pairs matrix exactly the same as in  original polystyrene melt, i.e., to keep all the related 1-2, 1-3, and 1-4 interactions centered around the removed backbone bonds  switched off, but 1-4 interactions are scaled by a factor of fudgeLJ=0.5.  To do so, I have tried in two different ways. (1) The bondtype of 5 is specified for all the removed backbone C-C bonds in *.top file, and all the related angles and dihedrals are removed form *.top file .  (2)  Truely delete these backbone bonds with the related angles and dihedrals from *.top file, and related  1-2, 1-3, and 1-4 interaction pairs are excluded by be listed in the section of "[ exclusions ]" in *.top file.  Both ways are giving exactly the same LJ(SR) and Coulomb(SR) energies in md.log file as in the case of pure polystyrene system before bond removing.  However, the simulation can only be performed in a serial way.  Once the simulation is performed in parallel, the simulaiton will stop after thounsands of steps with the following error information:

>Not all bonded interactions have been properly assigned to the domain decomposition cells 

>A list of missing interactions: 
>LJ-14 of 17640 missing 1 
>exclusions of 36480 missing 1 

>Molecule type 'Other' 
>the first 10 missing interactions, except for exclusions: 
>LJ-14 atoms 4727 4761 global 4727 4761

Atoms numbers of 4727 and 4761 are two randomly shown-up backbone carbons separated by a styrene unit. These atomic indices shown up in the erro message are different for different parallel runs starting from different initial configurations. 

It will be very grateful if any suggestions. 

With best regards,
Hu-Jun 



Dr. Hu-Jun Qian
Institute of Theoretical Chemistry, Jilin University
LiuTiao Road 2 #, Changchun, 130021, China
Tel: +86 431 8849 8132
Fax: +86 431 8849 8026
Email: hjqian at jlu.edu.cn;
          hujunqian at gmail.com
http://www.researcherid.com/rid/A-1683-2009