[gmx-users] once more: free energy and soft core question

[Frauke Meyer]

Hi,

is there somebody around with experience in soft core potentials and
free energy calculations? Haven't got any answer yet for my question
below..

What I find particularly strange is that with an initial lambda = 0 and
delta_lambda=0 as well (i.e. lambda stays zero during the MD, no
step-wise increase), the dH/dlambda heavily depends on if soft-core
potentials are used or not (sc_alpha=0 or sc_alpha!=0). But: should not
topology A be just hard-core (eq 4.103 in the manual) and the potential
of topology B (only dummies) anyway zero, thus the sum of both
independent from soft-core parameters?

Looking forward to some help,
Frauke 

topology for mutated ligand:
[ atoms ]
;   nr       type  resnr residue  atom   cgnr     charge       mass 
typeB    chargeB      massB
     1          H      1    BOM     H1      1      0.398      1.008 
DUM  0      1.008   ; qtot 0.398
     2         OA      1    BOM     O1      1     -0.548    15.9994 
DUM  0    15.9994   ; qtot -0.15
     3        CH2      1    BOM     C2      1       0.15     14.027 
DUM  0     14.027   ; qtot 0
     4        CH2      1    BOM     C4      2          0     14.027 
DUM  0     14.027   ; qtot 0
     5        CH2      1    BOM     C7      3          0     14.027 
DUM  0     14.027   ; qtot 0
     6        CH2      1    BOM    C10      4          0     14.027 
DUM  0     14.027   ; qtot 0
     7        CH2      1    BOM    C13      5          0     14.027 
DUM  0     14.027   ; qtot 0
     8        CH2      1    BOM    C16      6          0     14.027 
DUM  0     14.027   ; qtot 0
     9        CH2      1    BOM    C19      7          0     14.027 
DUM  0     14.027   ; qtot 0
    10        CH2      1    BOM    C22      8          0     14.027 
DUM  0     14.027   ; qtot 0
    11        CH2      1    BOM    C25      9          0     14.027 
DUM  0     14.027   ; qtot 0
    12        CH1      1    BOM    C28     10          0     13.019 
DUM  0     13.019   ; qtot 0
    13        CH1      1    BOM    C31     11          0     13.019 
DUM  0     13.019   ; qtot 0
    14        CH1      1    BOM    C33     12          0     13.019 
DUM  0     13.019   ; qtot 0
    15        CH1      1    BOM    C35     13          0     13.019 
DUM  0     13.019   ; qtot 0
    16        CH2      1    BOM    C37     14          0     14.027 
DUM  0     14.027   ; qtot 0
    17        CH2      1    BOM    C39     15          0     14.027 
DUM  0     14.027   ; qtot 0
    18        CH3      1    BOM    C42     16          0     15.035 
DUM  0     15.035   ; qtot 0



-------------------------------------------------------------------
Hi all,

for the perturbation of a ligand (A) to dummy atoms (B) I want to use
the
soft core potential. With

free_energy              = yes
init_lambda              = 0
delta_lambda             = 0.000001
sc-alpha                 = 1.5
sc-sigma                 = 0.3

I get LINCS warnings after the first few steps and mdrun crashes,
whereas
with

sc-alpha                 = 0
sc-sigma                 = 0.3

the whole perturbation runs fine (though with the expected singularities
for lambda near to 1).

Surprisingly, with larger sc-alpha (eg. 10) LINCS warnings are fewer and
stop after some steps, and the perturbation terminates normally.
What might the problem here be? Topology B (dummies covalently boudn to
each other) anyway has no dispersion. I expected less warnings and
similar
results to alpha=0 with *lowering* alpha, but did not find that.

Another surprise was that the dynamics depend on sc-sigma: Higher
sc-sigma
has the same effects a higher sc-alpha. But should not sigma_A be
calculated brom C6_A and C12_A, and sigma_B not play a role, because
C6_B = C12_B = 0 anyway, so that sc-alpha is not used for the distortion
of LJ?

Or what is my misunderstanding here?

Thanks for any advice,
cheers
Frauke