[gmx-users] The molecule size

主月 :) jiqing at iccas.ac.cn
Mon Sep 18 08:51:37 CEST 2006

> Hi:
> Two melt models were built for polyethylene (PE) and 
> polyvinylmethylether (PVME) melt with PBC condition .
> The density of both melt model agree with experimenal value well.But 
> when one check the radius of gyration (Rg) of them, both of them were 
> too small to accept as follows.
> The Rg for PE (C1000) is just 28 angstrom. It means the infinite 
> charaterastic ratio (Cinf) for the polymer is just about 2 which is much 
> smaller than scatter experimental value about 7.
> The Rg for PVME (C44) melt is about 6.6 angstrom. It means the Cinf for 
> the polymer is just 2.5 which is much smaller than scatter experimental 
> value 8-10.
> Can these results be accepted?
> Is there any fault in force field? gromos96a

Usually a garbage result as output means that you had either garbage as
input, or garbage for the algorithm. Find a published article that
describes a similar simulation and adapt their method suitably.
Otherwise describe your method more thoroughly (e.g. how large was the
box, what ensemble did you use, equilibration regime, etc.) and maybe
someone has some judgement they can share with you.


Hi Mark:
Thanks for your advise. Because the PE model is built by one of my officemate, i did not konw its details.

The cell length about my PVME model is 4.5 nm which is big enough for a PVME chain possesses all trans conformation. The ensemble is NVT with the control file Pcoupl = no after 10ns NPT simulation to reach the experimental density. The runtime for NVT is 5ns from which the relax time for end to end vector is anaylzed. The relax time  is about 1ns. So i think the system has been relaxed enough.

Is there any error in my process?

Maybe the residue parameter for PVME is also needed for discuss. They are:

[ VME ]   
[ atoms ]                                                
;   atom     type    charge  cgnr CN   Gasteiger     
     CAB   CH1     0.142     1  ;      CN
     CAA   CH2     0.035     1  ;      CN
     OAD    OE    -0.352     1  ;      CN
     CAC   CH3     0.174     1  ;      CN
[ bonds ]                                                                
; ai  aj  fu                                            
   CAA   CAB   gb_27          
   CAB   OAD   gb_53          
   CAC   OAD   gb_53     
   CAB  +CAA   gb_27    
[ angles ]                                                                     
; ai  aj  ak  fu    c0, c1, ...                                                
   CAA   CAB   OAD   ga_30  
   CAB   OAD   CAC   ga_10 
   OAD   CAB  +CAA   ga_30
   CAA   CAB  +CAA   ga_15
   CAB  +CAA  +CAB   ga_15 

[ dihedrals ]
; ai  aj  ak  al  fu    c0, c1, m, ...
  CAA  CAB  OAD  CAC   gd_13
  CAA  CAB +CAA +CAB   gd_34
 +CAA  CAB  OAD  CAC   gd_13
 CAB  +CAA +CAB +OAD    gd_1

Ji Qing
Institute of Chemistry, Chinese Academy of Sciences
Tel: 0086-10-62562894  ,82618423
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20060918/fe2ea449/attachment.html>

More information about the gromacs.org_gmx-users mailing list