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<DIV><FONT size=2>Thanks very much for your patient explaination.It really is a
question confusing me much. What I am interested in is inserting some organic
molecules into lipid bilayers. Tieleman's lipid parameters have given out the
interactive LJ parameters with ffgmx forcefield. So if I want to simulate lipid
with tileman's force field I should use ffgmx for organic molecules. However I
have to prove the ffgmx forcefield for organic molecules is correct too.
Somebody prove this by calculating the new molecules' melting point or their
structures in solutions to compare with X-ray results. I found <BR>Monika
Holtje's BBA article(Biochimica et Biophysica Acta 1511 (2001) 156^167), they
simulated cholesterol and stearic acid and palmitic acid, constructing topology
files using Gromos 87 forcefield , and put the Cholesterol topology on Gromacs
website.They said " The geometries, conformations and configurations as they
occur instandard GROMACS dynamics in vacuo and in water using the parameter set
in this file, compared well with crystal structures". In their topology , they
set the partial charge like this:</FONT></DIV>
<DIV><FONT size=2></FONT> </DIV>
<DIV> </DIV>
<DIV><FONT size=2>; nr type
resnr residu atom
cgnr charge ; total
charge<BR> 1
CH3 1
CHOL C1
1 0<BR>
2 CB
1 CHOL
C2 2
0<BR> 3
CH2 1
CHOL C3
3 0<BR>
4 CH2
1 CHOL
C4 4
0<BR> 5
CH1 1
CHOL C5
5 0.14 ; charges adopted<BR>
6 OA
1 CHOL
O6 5 -0.54 ; from
Retinol in<BR> 7
HO 1
CHOL H
5 0.40 ; ffgmx.rtp<BR>
8 CH2
1 CHOL
C8 6
0<BR> 9
CB 1
CHOL C9
7 0<BR> 10
CR61 1
CHOL C10
8 0<BR> 11
CH2 1
CHOL C11
9 0<BR> 12
CH1 1
CHOL C12
10 0<BR> 13
CH1 1
CHOL C13
11 0<BR> 14
CH2 1
CHOL C14
12 0<BR> 15
CH2 1
CHOL C15
13 0<BR>
16 CB
1 CHOL
C16 14
0<BR> 17
CH3 1
CHOL C17
15 0<BR> 18
CH1 1
CHOL C18
16 0<BR> 19
CH2 1
CHOL C19
17 0<BR> 20
CH2 1
CHOL C20
18 0<BR> 21
CH1 1
CHOL C21
19 0<BR> 22
CH1 1
CHOL C22
20 0<BR> 23
CH3 1
CHOL C23
21 0<BR> 24
CH2 1
CHOL C24
22 0<BR> 25
CH2 1
CHOL C25
23 0<BR> 26
CH2 1
CHOL C26
24 0<BR> 27
CH1 1
CHOL C27
25 0<BR> 28
CH3 1
CHOL C28
26 0<BR> 29
CH3 1
CHOL C29
27 0</FONT></DIV>
<DIV><FONT size=2></FONT> </DIV>
<DIV><FONT size=2>However when I use B3lyp/6-31G(d,p) to calculate mulliken
distribution of cholesterol the charge distribution is rather different.
How did they decide their partial charge? Is it customed to let alkane
groups zero charged? Many articles didn't give out the validation procedure of
their topologies in detail, are there some classic articles explaining
how the forcefield we used today, such as OPLS, GROMOS, AMBER and CHARMM ,
developed? I want to know how they were deduced from the very
beginning.</FONT></DIV>
<DIV><FONT size=2></FONT> </DIV>
<DIV><FONT size=2>Any suggestion will be appreciated , thanks very much in
advance.</FONT></DIV>
<DIV><FONT size=2> </DIV>
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