[gmx-users] bug/help - pure charge transformation using fep-lambdas=1.0

[Camila Zanette]

Dear all,

I am trying to run a simulation using morse potential where I do a pure
charge transformation of two atom of my molecule. The only thing my
topology file is saying is to change the hydrogens (27 and 28) charges from
0.0 to 0.03695.

[ atoms ]
;   nr       type  resnr    res   atom   cgnr     charge       mass
 typeB    chargeB      massB comments
     1         c3      1    MOL     C1      1   -0.07090  12.000000
c3   -0.07090  12.000000 ; MCSS
     2         c3      1    MOL     C2      2   -0.06840  12.000000
c3   -0.06840  12.000000 ; MCSS
(...)
    26         hc      1    MOL    H16     26    0.03695   1.000000
hc    0.03695   1.000000 ; MCSS
    27         hc      1    MOL    H17     27    0.00000   1.000000
hc    0.03695   1.000000 ; to be appeared
    28         hc      1    MOL    H18     28    0.00000   1.000000
hc    0.03695   1.000000 ; to be appeared

I am using just five lambda values (coul-lambdas) of 0.0, 0.25, 0.5, 0.75,
and 1.0.

fep_lambdas              = 1.0 1.00 1.0 1.00 1.0
vdw_lambdas              = 1.0 1.00 1.0 1.00 1.0
coul_lambdas             = 0.0 0.25 0.5 0.75 1.0
mass-lambdas             = 0.0 0.00 0.0 0.00 0.0

Setting the fep-lambdas all 1.0, we found a "bug" in the .xvg files where
there are multiples "zeros" interleaved with "non-zeros" values. This case
only occurred with the vacuum simulation, the water simulation was OK. Here
are the contents of one of the .xvg files for free energy:

52.8000 -4176.0000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
0.0000000 0.0000000 0.0000000
52.9000 -4176.0000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
0.0000000 0.0000000 0.0000000
53.0000 -4176.0000 0.0000000 0.086857602 0.0000000 0.0000000 0.021714401
0.043428800 0.065143197 0.086857601
53.1000 -4176.0000 0.0000000 0.088871211 0.0000000 0.0000000 0.022217803
0.044435606 0.066653397 0.088871207


If we changed the fep-lambdas to 0, we don't get those "zeros" there.

Does someone know what is happening here?


Thank you very much!


PS: Here are the files in case someone wants to reproduce the problem and
also check my .xvg files:
https://www.dropbox.com/sh/r3yzr1zzhuc996f/AABKRQXkp4-N5Ep1o-AVn3Yoa?dl=0
The folder mdp_files_fep0 is the one where the fep-lambdas are all 0 and
the data_fep0 contains the .xvg files for this running. The same works for
mdp_files_fep1 and data_fep1 for fep-lambdas equal to 1. Under run_scripts
are my job scripts for the simulation.
-- 
Camila Zanette