I already checked the unit and the values of A and B Coeff.
And this is my parameter setup both on amber and gromacs.
--------------------------------
¥ò (Å) ¥å (kJ/mol) ¥å (kcal/mol) A B ACOEFF BCOEFF
3.2823 0.4839 0.1156 1.808E+05 2.892E+02 7.234E+05 5.784E+02
3.2823 0.3000 0.0717 1.121E+05 1.793E+02 4.485E+05 3.587E+02
3.2823 0.3500 0.0837 1.308E+05 2.092E+02 5.232E+05 4.184E+02
3.2823 0.4000 0.0956 1.495E+05 2.391E+02 5.980E+05 4.782E+02
3.2823 0.4500 0.1076 1.682E+05 2.690E+02 6.727E+05 5.380E+02
3.2823 0.5000 0.1195 1.869E+05 2.989E+02 7.475E+05 5.978E+02
3.2823 0.5500 0.1315 2.056E+05 3.288E+02 8.222E+05 6.575E+02
--------------------------------------------------------
Thanks.
Bongkeun Kim
bkim at chem.ucsb.edu
Quoting InSuk Joung <i.joung.gmail.com>:
> Hi,
> As fas as I know, your way to modify the topology file is correct although
> you should be careful as the system gets more complicated.
>
> I have some suggestions you can try. First, make sure that A and B
> coefficients are calculated with units of Angstrom and kcal/mol (not
> kJ/mol). You probably understand that you only tried to modify C-O
> interactions not C-C interactions. Double-check if it is the same in your
> GROMACS setup.
>
> On Wed, Jul 27, 2011 at 12:58 PM, <bkim.chem.ucsb.edu> wrote:
>
>> Hello,
>>
>> I am running a simulation which has only carbon atoms(graphite) and SPC/E
>> water molecules to calculate the contact angle in NVT.
>> I made the different sets of input files with different prmtop files in
>> which the L-J parameter between carbons and oxygens.
>>
>> In each prmtop file, I have only 3 atom types (C, O and H) and the non
>> bonded parm index is given as
>> ---------------
>> FLAG NONBONDED_PARM_INDEX
>> %FORMAT(10I8)
>> 1 2 4 2 3 -1 4 -1 6
>> ----------------
>>
>> So the L-J parameter for C-O are in the second position in each A and B
>> coeff.
>> ----------
>> %FLAG LENNARD_JONES_ACOEF
>> %FORMAT(5E16.8)
>> 8.19971662E+05 7.23869979E+05 6.29362166E+05 0.00000000E+00
>> 0.00000000E+00
>> 0.00000000E+00
>> %FLAG LENNARD_JONES_BCOEF
>> %FORMAT(5E16.8)
>> 5.31102864E+02 5.78465890E+02 6.25267765E+02 0.00000000E+00
>> 0.00000000E+00
>> 0.00000000E+00
>> %FLAG
>> -------------------
>>
>> I changed the second coefficients from epsilon values varying from
>> 0.3kJ/mol to 0.5kJ/mol and also from sigma values from 3.0A to 3.3A. I
>> checked the amber FAQ to convert these values to the ones of r and epsilon
>> and to 12-6 A and B coefficients.
>>
>> But I have currently no changes in contact angles from 14 different runs.
>> The average WCA only changes +-1 degrees with different L-J parameters.
>> But in my previous simulations in GROMACS which I modified sigma and
>> epsilon values only on carbon atoms(there is no option to define pair
>> parameter in topology file) can show about +-10 degree changes for total
>> set of different parameters.
>>
>> Is there any other parameter that I need to change in the prmtop file?
>> Thank you.
>> Bongkeun Kim
>> bkim at chem.ucsb.edu
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> Best,
> InSuk Joung
> _______________________________________________
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> AMBER.ambermd.org
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>
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Received on Wed Jul 27 2011 - 12:30:04 PDT
