Yes, I used the last two numbers for prmtop file. The numbers in
column A and B are used to conversion from gromacs to amber.
Thanks.
Bongkeun Kim
Quoting InSuk Joung <i.joung.gmail.com>:
> I don't know about GROMACS but, as I said, the numbers in the last two
> columns are the numbers that need go to the "AMBER" topology files. If you
> used numbers in the columns of 'A' and 'B', your numbers were wrong.
>
> 2011/7/27 Bongkeun Kim <bkim.chem.ucsb.edu>
>
>> 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
>> >> 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 - 14:30:02 PDT
