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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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