[gmx-users] The molecule size

[Mark Abraham]

主月 ：） wrote:
> 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.

Mark