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

[Jochen Hub]

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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-- 
************************************************
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
************************************************