[gmx-users] Re: The molecule size (jiqing)
jiqing at iccas.ac.cn
Tue Sep 19 04:01:06 CEST 2006
> > 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
- 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.
> 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
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