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
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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