[gmx-users] Non-attractive Lennard-Jones
Dahlia Weiss
dweiss at stanford.edu
Wed Apr 27 21:09:57 CEST 2005
The LJ matrix looks correct according to the parameters that I put in.
functype[0]=LJ_SR, c6= 0.00000000e+00, c12= 3.37400002e-06
functype[1]=LJ_SR, c6= 0.00000000e+00, c12= 2.98061718e-06
functype[2]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
functype[3]=LJ_SR, c6= 0.00000000e+00, c12= 2.98061718e-06
functype[4]=LJ_SR, c6= 2.61710002e-03, c12= 2.63309994e-06
functype[5]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
functype[6]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
functype[7]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
functype[8]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
When I looked at other force fields, for example at ffgmxnb.itp, the C6
and C12 parameters look the same as what I gave. However, the
interaction parameter between carbon and oxygen is completely
different.
ffgmxnb.itp
--------------
[ atomtypes ]
;name mass charge ptype c6 c12
OW 15.99940 0.000 A 0.26171E-02 0.26331E-05
CB 12.01100 0.000 A 0.23402E-02 0.33740E-05
[ nonbond_params ]
; i j func c6 c12
OW CB 1 0.24748E-02 0.15818E-05
CB CB 1 0.23402E-02 0.33740E-05
OW OW 1 0.26171E-02 0.26331E-05
As you can see in ffgmxnb.itp c12(OW CB) does not equal
(c12(OW)*c12(CB) )^ 1/2, which is what I thought. Is this because of
some difference between the GMX and OPLS force-field? Or is this some
problem in my simulation?
It looks like the repulsive term in my simulation is too strong. Is it
possible to set the non-bond params in the OPLS force-field? I tried
pasting the [ nonbond_params ] section into my ffoplsaanb.itp file, but
this didn't work.
Thank you for all your help,
Dahlia Weiss
On Apr 25, 2005, at 11:40 PM, David van der Spoel wrote:
> On Mon, 2005-04-25 at 14:24 -0700, Dahlia Weiss wrote:
>> I am running a simulation with only carbon (in the form of a
>> hydrocarbon) and water in the OPLS-AA force field. I wanted to "turn
>> off" the attractive part of the carbon-oxygen Lennard-Jones force,
>> which I did by setting the C6 parameter of carbon to zero. I changed
>> the combination rule to 1 and left the gen-pairs option as yes in the
>> ffoplsaa.itp file. The results were not what I expected. I ran the
>> same
>> experiment in another force-field using different software and the
>> results were more like what I would have expected. I therefore
>> conclude
>> that I did not succeed in turning off only the LJ carbon-oxygen
>> attraction.
>>
>> I obtained the c6 and c12 parameters through the equations:
>> c6(i) = epsilon(i)*sigma(i)^6
>> c12(i) = epsilon(i)*sigma(i)^12
>> Perhaps this is the problem?
>
> Not necessarily. Checkt your tpr file before use with the gmxdump
> utility to see what the parameters look like. Do
> gmxdump -s topol.tpr | less
> and search for idef (interaction definition). There you'll find the LJ
> matrix.
>
>>
>>
>> Below are the files that I changed.
>>
>> ffoplsaa_hs.itp
>> -------------------
>>
>> #define _FF_OPLS
>> #define _FF_OPLSAA
>>
>> [ defaults ]
>> ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
>> 1 1 yes 0.5 0.5
>>
>> #include "ffoplsaanb_hs.itp"
>> #include "ffoplsaabon_hs.itp"
>>
>>
>> ffoplsaanb_hs.itp
>> -----------------
>> [ atomtypes ]
>> ;name bond_type mass charge ptype c6 c12
>>
>> opls_501 CB 12.01100 0.000 A 0.00000E+00 4.69340E-06
>> opls_116 OW 15.99940 0.000 A 2.60000E-03 2.63350E-06
>> opls_117 HW 1.00800 0.000 A 0.00000E+00 0.00000E+00
>>
>>
>> ffoplsaabon_hs.itp
>> ------------------
>> [ bondtypes ]
>> ; i j func b0 kb
>> OW HW 1 0.09572 502080.0
>> CB CB 1 0.13900 502080.0
>>
>>
>> [ angletypes ]
>> ; i j k func tHC cth
>> CB CB CB 1 120.000 418.400
>> HW OW HW 1 109.500 502.080
>>
>>
>> [ dihedraltypes ]
>> ; i j k l func coefficients
>> X CB CB X 3 30.33400 0.00000 -30.33400
>> 0.00000 0.00000 0.00000 ; aromatic ring
>>
>>
>> Thank you,
>> Dahlia Weiss
>>
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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
> spoel at xray.bmc.uu.se spoel at gromacs.org
> http://xray.bmc.uu.se/~spoel
> +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> +
>
>
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------- ** -------
Dahlia Weiss
Levitt Lab, Clark S210
Stanford University
Stanford CA 94305-5080
USA
lab phone: 650-725-0754
dweiss at stanford.edu
http://www.stanford.edu/~dweiss
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