Eudes Fileti wrote:
Dear gmx users
I have attemped to simulate a box of ethanol in normal conditions of
temperature and pressure.
I reproduced very well some literature data (as g(r)) however I had
problems to reproduce the angular
distribution function for the dihedral (C-C-O-H).
This angle must have a peak in 180 degrees and two lesser (and
symmetrical) peaks in 60 and 300 degrees (as shows the figure 1 of this
link http://cbio.mskcc.org/~leonor/jpcb97.pdf ).
However my distribution presents a maximum in 100 degrees with two (but
not symmetrical) peaks the left.
I already made almost everything:
I used both, dihedral GROMACS and Ryckaert-Bellemans, I applied almost
all the avaliables parameters
(eg in ffoplsaabon.itp), I set nrexcl 2, 3, 4, 5, I remade the
simulation several times in with differents conditions, but always I
found the same pattern.
Somebody already had some experience like that? If it had, could you
give me a insight? Bellow I give my top file.
Thank you in advance.
eef
;
; File 'etanol.top' was generated
; By user: fileti (1000)
; On host: linux
; At date: Sat Jul 15 16:41:25 2006
;
; This is your topology file
; "Out Of Register Space (Ugh)" (Vi)
;
; Include forcefield parameters
#include "ffoplsaa.itp"
[ moleculetype ]
; Name nrexcl
ETH 2
[ atoms ]
; nr type resnr residue atom cgnr charge mass
typeB chargeB massB
1 opls_135 1 EtOH CB 1 -0.18 12.011 ;
qtot -0.18
2 opls_140 1 EtOH HB1 1 0.06 1.008 ;
qtot -0.12
3 opls_140 1 EtOH HB2 1 0.06 1.008 ;
qtot -0.06
4 opls_140 1 EtOH HB3 1 0.06 1.008 ;
qtot 0
5 opls_157 1 EtOH CA 2 0.145 12.011 ;
qtot 0.145
6 opls_140 1 EtOH HA1 2 0.06 1.008 ;
qtot 0.205
7 opls_140 1 EtOH HA2 2 0.06 1.008 ;
qtot 0.265
8 opls_154 1 EtOH OH 2 - 0.683 15.9994 ;
qtot -0.418
9 opls_155 1 EtOH HO 2 0.418 1.008 ;
qtot 0
[ bonds ]
; ai aj funct c0 c1
1 2 1 0.10800 284512.0
1 3 1 0.10800 284512.0
1 4 1 0.10800 284512.0
1 5 1 0.14040 392459.2
5 6 1 0.10800 307105.6
5 7 1 0.10800 307105.6
5 8 1 0.13640 376560.0
8 9 1 0.09450 462750.4
[ angles ]
; ai aj ak funct c0 c1
2 1 3 1 107.800 276.144
2 1 4 1 107.800 276.144
2 1 5 1 107.800 276.144
3 1 4 1 107.800 276.144
3 1 5 1 110.700 313.800
4 1 5 1 110.700 313.800
1 5 6 1 109.500 292.880
1 5 7 1 109.500 292.880
1 5 8 1 109.500 418.400
6 5 7 1 107.800 276.144
6 5 8 1 115.000 334.720
7 5 8 1 108.000 585.760
5 8 9 1 109.000 292.880
[ dihedrals ]
; ai aj ak al funct c0 c1 c2
c3 c4 c5
2 1 5 6 3 1.67360 -1.67360 0.00000
0.00000 0.00000 0.00000
2 1 5 7 3 1.67360 -1.67360 0.00000
0.00000 0.00000 0.00000
2 1 5 8 3 0.97905 2.93716 0.00000
-3.91622 0.00000 0.00000
3 1 5 6 3 1.67360 -1.67360 0.00000
0.00000 0.00000 0.00000
3 1 5 7 3 1.67360 -1.67360 0.00000
0.00000 0.00000 0.00000
3 1 5 8 3 0.97905 2.93716 0.00000
-3.91622 0.00000 0.00000
4 1 5 6 3 1.67360 -1.67360 0.00000
0.00000 0.00000 0.00000
4 1 5 7 3 1.67360 -1.67360 0.00000
0.00000 0.00000 0.00000
4 1 5 8 3 0.97905 2.93716 0.00000
-3.91622 0.00000 0.00000
1 5 8 9 3 26.15000 -3.13800 -23.01200
0.00000 0.00000 0.00000
6 5 8 9 3 0.94140 2.82420 0.00000
-3.76560 0.00000 0.00000
7 5 8 9 3 0.94140 2.82420 0.00000
-3.76560 0.00000 0.00000
______________________________________
Eudes Eterno Fileti
Centro de Ciência Naturais e Humanas
Universidade Federal do ABC
Rua Santa Adélia, 166
CEP 09210-170
skype: eefileti
------------------------------------------------------------------------
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--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
;
; Ethanol, Jorgensen et al. JACS 118 pp. 11225 (1996)
;
[ moleculetype ]
; name nrexcl
ETH 3
[ atoms ]
; nr type resnr residu atom cgnr charge mass
1 opls_157 1 ETH C 1 -0.18
2 opls_156 1 ETH H 1 0.06
3 opls_156 1 ETH H 1 0.06
4 opls_156 1 ETH H 1 0.06
5 opls_157 1 ETH C 2 0.145
6 opls_156 1 ETH H 2 0.06
7 opls_156 1 ETH H 2 0.06
8 opls_154 1 ETH OA 2 -0.683
9 opls_155 1 ETH HO 2 0.418
[ bonds ]
; ai aj funct c0 c1
1 5 1
3 1 1
4 1 1
2 1 1
7 5 1
6 5 1
8 5 1
9 8 1
[ pairs ]
; i j func
2 6
2 7
2 8
3 6
3 7
3 8
4 6
4 7
4 8
1 9
6 9
7 9
[ angles ]
; ai aj ak funct c0 c1
; H3
2 1 5 1
3 1 5 1
4 1 5 1
;
4 1 3 1
4 1 2 1
;
3 1 2 1
;
1 5 7 1
1 5 6 1
1 5 8 1
;
5 8 9 1
;
6 5 7 1
6 5 8 1
;
7 5 8 1
;
[ dihedrals ]
2 1 5 8 3
3 1 5 8 3
4 1 5 8 3
1 5 8 9 3
6 5 8 9 3
7 5 8 9 3
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