Yes, I used that equation for comparison with gromacs.
Bongkeun Kim
Quoting InSuk Joung <i.joung.gmail.com>:
> If your sigma is the one in the equation,
> V(LJ) = 4 *epsilon ( (sigma/r)^12 - (sigma/r)^6 )
>
> ACOEFF and BCOEFF in your table (last two columns) are the correct numbers
> you need to put in the AMBER topology file.
>
> 2011/7/27 Bongkeun Kim <bkim.chem.ucsb.edu>
>
>> 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
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>>
>>
>>
>>
>> _______________________________________________
>> AMBER mailing list
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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> Best,
> InSuk Joung
> _______________________________________________
> AMBER mailing list
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>
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Received on Wed Jul 27 2011 - 13:00:33 PDT
