[gmx-users] free energy and soft core

[Frauke Meyer]

Dear Berk,

> >free_energy              = yes
> >init_lambda              = 0
> >delta_lambda             = 0
> >
> >
 >
> >
> >dG/dl is different for both, which is alright.
> >                 alpha=0        alpha=1.5
> >                 @TYPE xy        @TYPE xy
> >                 0 173.378       0 173.378
> >                 0.002 170.874   0.002 -7.056
> >                 0.004 168.351   0.004 -7.9578
> >                 0.006 166.028   0.006 -8.24761
> >                 ....
> >
> >
> >But should not the potential energy itself be identical for lambda=0?
> >What am I doing wrong?
> 
> Are the above results with delta-lambda=0?
> If delta-lambda=0 and thus lambda=0 the results should be
> identical, including dvdlambda. mdrun will use the non-softcore
> innerloops for lambda=0, so the results should really be identical.
> But from the huge jump from t=0 to 0.002 I would guess delta-lambda
> is not zero.
> I just recalled that I have fixed a bug in cvs with free-energy
> and rcoulomb<rvdw. But as far as I know this bug always caused
> a segmentation violation.
> Is rcoulomb<rvdw in your simulations?
> 
> >

Yes above results are for delta-lambda=0 - that is what I am wondering
about. As a test I did the same without solvent, one molecule in a box
without pbc, but have the same difference when I change from hard-core
to soft-core
alpha=0         alpha=1.5
0 12.7774       0 12.7774
0.002 12.3728   0.002 -3.20253
0.004 11.9785   0.004 -3.6638
0.006 11.6088   0.006 -4.07433
0.008 11.2765   0.008 -4.41497
0.01 10.9911    0.01 -4.67666

My molecule just has a few charges of which the interaction are excluded
(Coulomb1-4=CoulombLR=CoulombSR = 0), so it's all about the LJ
interactions within the molecule.
I could reproduce the bug that you mentioned if rcoulomb<rvdw. 
This looks to me like another bug..?


This is my topology:
[ 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


Frauke