[gmx-users] The molecule size

[David van der Spoel]

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

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?


> 
> 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:*
> ** 

-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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