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

[friendli]

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 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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