[gmx-users] Rugged dgdl curve in turning off/on the charge for Leu

[friendli]

thank you for the rational explanation.
but is the free energy change in the charge on/off step(~10kJ/mol) small
enough to ignore the flucturations?  The free energy change in the LJ
mutation step is about 8kJ/mol.

On Fri, Jan 16, 2009 at 11:56 PM, Jochen Hub <jhub at gwdg.de> wrote:

> friendli wrote:
> > Dear all,
> >
> > When I performing mutation free energy calculation from Leu to  Ala, I
> > first turn off the charge on the side chain of Leu. As I read from the
> > GMX archive, the dG/dl curve should be rather smooth for turning off the
> > partial charge.
> > In this step(charge off/on), however, I can not obtain the expected
> > smooth dGdl curve.(see the attachment). I did not use soft-core in this
> > step.
> > Is this normal because the mutation is relatively large? If not, what
> > could be the problem?
>
> The partial charges of the sidechaines of apolar AA (such as Leu) are
> almost zero, that's why your dGdl is almost zero. Only because of the
> small dgdl your curve looks non-smooth, but that's just a scale issue here.
>
> Best,
> Jochen
>
> >
> >
> > the following is part of the topology file.
> >
> >    17   opls_238      2    LEU      N      7       -0.5    14.0067   ;
> > qtot 0.5
> >    18   opls_241      2    LEU      H      7        0.3      1.008   ;
> > qtot 0.8
> >    19  opls_224B      2    LEU     CA      7       0.14     12.011   ;
> > qtot 0.94
> >    20   opls_140      2    LEU     HA      7       0.06      1.008   ;
> > qtot 1
> >    21   opls_136      2    LEU     CB      8      -0.12     12.011
> > opls_136    0     12.011 ; qtot 0.88
> >    22   opls_140      2    LEU    HB1      8       0.06      1.008
> > opls_140    0      1.008 ; qtot 0.94
> >    23   opls_140      2    LEU    HB2      8       0.06      1.008
> > opls_140    0      1.008 ; qtot 1
> >    24   opls_137      2    LEU     CG      9      -0.06     12.011
> > opls_137    0     12.011 ; qtot 0.94
> >    25   opls_140      2    LEU     HG      9       0.06      1.008
> > opls_140    0      1.008 ; qtot 1
> >    26   opls_135      2    LEU    CD1     10      -0.18     12.011
> > opls_135    0     12.011 ; qtot 0.82
> >    27   opls_140      2    LEU   HD11     10       0.06      1.008
> > opls_140    0      1.008 ; qtot 0.88
> >    28   opls_140      2    LEU   HD12     10       0.06      1.008
> > opls_140    0      1.008 ; qtot 0.94
> >    29   opls_140      2    LEU   HD13     10       0.06      1.008
> > opls_140    0      1.008 ; qtot 1
> >    30   opls_135      2    LEU    CD2     11      -0.18     12.011
> > opls_135    0     12.011 ; qtot 0.82
> >    31   opls_140      2    LEU   HD21     11       0.06      1.008
> > opls_140    0      1.008 ; qtot 0.88
> >    32   opls_140      2    LEU   HD22     11       0.06      1.008
> > opls_140    0      1.008 ; qtot 0.94
> >    33   opls_140      2    LEU   HD23     11       0.06      1.008
> > opls_140    0      1.008 ; qtot 1
> >    34   opls_235      2    LEU      C     12        0.5     12.011   ;
> > qtot 1.5
> >    35   opls_236      2    LEU      O     12       -0.5    15.9994   ;
> > qtot 1
> >
> > thank you
> >
> > Qiang
> >
> >
> >
> >
> > ------------------------------------------------------------------------
> >
> >
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> >
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>
> --
> ************************************************
> Dr. Jochen Hub
> Max Planck Institute for Biophysical Chemistry
> Computational biomolecular dynamics group
> Am Fassberg 11
> D-37077 Goettingen, Germany
> Email: jhub[at]gwdg.de
> Tel.: +49 (0)551 201-2312
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