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<DIV>Hi:<BR>> > <BR>> > Two melt models were built for
polyethylene (PE) and<BR>> > polyvinylmethylether (PVME) melt with
PBC condition .<BR>> > <BR>> > The density of both melt
model agree with experimenal value well.But<BR>> > when one check
the radius of gyration (Rg) of them, both of them were<BR>> > too
small to accept as follows.<BR>> > <BR>> > The Rg for PE
(C1000) is just 28 angstrom. It means the infinite<BR>> >
charaterastic ratio (Cinf) for the polymer is just about 2 which is
much<BR>> > smaller than scatter experimental value about
7.<BR>> > <BR>> > The Rg for PVME (C44) melt is about
6.6 angstrom. It means the Cinf for<BR>> > the polymer is just 2.5
which is much smaller than scatter experimental<BR>> > value
8-10.<BR>> > <BR>> > Can these results be
accepted?<BR>> > <BR>> > Is there any fault in force
field? gromos96a<BR><BR>Two things,<BR><BR>- maybe you need a larger
systems<BR>- maybe g_gyrate does not take periodicity into account correctly.
<BR>extract some single molecules and look at them in a viewer, or write
<BR>your own script to compute Rg.<BR>- have you used pbc = full for the
simulations?</DIV>
<DIV> </DIV>
<DIV><FONT face=ΣΧΤ² color=#008000>1.<STRONG><FONT size=5>The cell length about my
PVME model is 4.5 nm which is big enough for a PVME chain possesses all trans
conformation.</FONT></STRONG></FONT></DIV>
<DIV><STRONG><FONT face=ΣΧΤ² color=#008000 size=5></FONT></STRONG> </DIV>
<DIV><STRONG><FONT face=ΣΧΤ² color=#008000 size=5>2. The Rg is anaylzed by my own
program, which has been validated.</FONT></STRONG></DIV>
<DIV><STRONG><FONT face=ΣΧΤ² color=#008000 size=5></FONT></STRONG> </DIV>
<DIV><STRONG><FONT face=ΣΧΤ² color=#008000 size=5>3.PBC=XYZ</FONT></STRONG></DIV>
<DIV><BR><BR><BR>> <BR>> Usually a garbage result as output means that you
had either garbage as<BR>> input, or garbage for the algorithm. Find a
published article that<BR>> describes a similar simulation and adapt their
method suitably.<BR>> Otherwise describe your method more thoroughly (e.g.
how large was the<BR>> box, what ensemble did you use, equilibration regime,
etc.) and maybe<BR>> someone has some judgement they can share with
you.<BR>> <BR>> Mark<BR>> <BR>> *Hi Mark:*<BR>> *Thanks for
your advise. Because the PE model is built by one of my <BR>> officemate, i
did not konw its details.*<BR>> ** <BR>> *The cell length about my PVME
model is 4.5 nm which is big enough for a <BR>> PVME chain possesses all
trans conformation. The ensemble is NVT with <BR>> the control file Pcoupl =
no after 10ns NPT simulation to reach the <BR>> experimental density. The
runtime for NVT is 5ns from which the relax <BR>> time for end to end vector
is anaylzed. The relax time is about 1ns. So <BR>> i think the system
has been relaxed enough.*<BR>> ** <BR>> *Is there any error in my
process?*<BR>> ** <BR>> *Maybe the residue parameter for PVME is also
needed for discuss. They are:*<BR>> </DIV>
<DIV><FONT face=ΣΧΤ² color=#008000 size=5><STRONG>[ VME ] <BR>[ atoms
]
<BR>; atom type
charge cgnr CN Gasteiger
<BR> CAB CH1
0.142 1 ;
CN<BR> CAA CH2
0.035 1 ;
CN<BR> OAD OE
-0.352 1 ;
CN<BR> CAC CH3
0.174 1 ;
CN<BR> <BR>[ bonds
]
<BR>; ai aj
fu
<BR> CAA CAB
gb_27 <BR>
CAB OAD
gb_53 <BR>
CAC OAD gb_53 <BR>
CAB +CAA gb_27
<BR> <BR>[ angles
]
<BR>; ai aj ak fu c0, c1,
...
<BR> CAA CAB OAD ga_30
<BR> CAB OAD CAC ga_10
<BR> OAD CAB +CAA
ga_30<BR> CAA CAB +CAA
ga_15<BR> CAB +CAA +CAB ga_15
</STRONG></FONT></DIV>
<DIV><FONT color=#008000 size=5><STRONG></STRONG></FONT> </DIV>
<DIV><FONT face=ΣΧΤ²><FONT color=#008000 size=5><STRONG> <BR>[
dihedrals ]<BR>; ai aj ak al fu c0,
c1, m, ...<BR> CAA CAB OAD CAC
gd_13<BR> CAA CAB +CAA +CAB gd_34<BR> +CAA
CAB OAD CAC gd_13<BR> CAB +CAA +CAB
+OAD gd_1</STRONG></FONT></DIV>
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