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<DIV><FONT face=ΣΧΤ² color=#008000><FONT color=#000000>> 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>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</FONT></FONT></DIV>
<DIV><FONT face=ΣΧΤ² color=#008000><FONT color=#000000></FONT></FONT> </DIV>
<DIV><FONT face=ΣΧΤ² color=#008000 size=5><STRONG>Hi Mark:</STRONG></FONT></DIV>
<DIV><FONT face=ΣΧΤ² color=#008000 size=5><STRONG>Thanks for your advise. Because
the PE model is built by one of my officemate, i did not konw its
details.</STRONG></FONT></DIV>
<DIV><FONT face=ΣΧΤ² color=#008000 size=5><STRONG></STRONG></FONT> </DIV>
<DIV><FONT face=ΣΧΤ² color=#008000 size=5><STRONG>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.</STRONG></FONT></DIV>
<DIV><STRONG><FONT face=ΣΧΤ² color=#008000 size=5></FONT></STRONG> </DIV>
<DIV><STRONG><FONT face=ΣΧΤ² color=#008000 size=5>Is there any error in my
process?</FONT></STRONG></DIV>
<DIV><FONT face=ΣΧΤ² color=#008000 size=5><STRONG></STRONG></FONT> </DIV>
<DIV><FONT face=ΣΧΤ² color=#008000 size=5><STRONG>Maybe the residue parameter for
PVME is also needed for discuss. They are:</STRONG></FONT></DIV>
<DIV><FONT face=ΣΧΤ² color=#008000 size=5><STRONG></STRONG></FONT> </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>
<DIV><BR><FONT color=#008000 size=5><STRONG> </STRONG></FONT></FONT></DIV>
<DIV><FONT face=ΣΧΤ² color=#008000
size=5><STRONG>*************************************************<BR>Ji
Qing<BR>Institute of Chemistry, Chinese Academy of Sciences<BR>Tel:
0086-10-62562894
£¬82618423<BR>*************************************************</STRONG></FONT></DIV></BODY></HTML>