[gmx-users] Re: The molecule size (jiqing)

[主月 ：）]

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

Two things,

- maybe you need a larger systems
- maybe g_gyrate does not take periodicity into account correctly. 
extract some single molecules and look at them in a viewer, or write 
your own script to compute Rg.
- have you used pbc = full for the simulations?

1.The cell length about my PVME model is 4.5 nm which is big enough for a PVME chain possesses all trans conformation.

2. The Rg is anaylzed by my own program, which has been validated.

3.PBC=XYZ



> 
> 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.
> 
> Mark
>  
> *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



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