[gmx-users] pull code absolute reference artifacts

[chris.neale at utoronto.ca]

Hello,

I have a question about the following grompp 4.0.4 warning:

"You are using an absolute reference for pulling, but the rest of the  
system does not have an absolute reference. This will lead to  
artifacts."

While I do realize that this is an excellent error message containing  
lots of information, I am still unclear about how to proceed. Why does  
my system not have an absolute reference? Is it because I have pbc and  
center of mass motion removal? Exactly what types of artifacts are  
expected? Is there a simple solution?

I am trying to hold my peptide in the center of a water box. I realize  
that there is no "center" and everything in pbc, but I need to do it  
nevertheless.

Here are my .mdp options:

pull                = umbrella
pull_geometry       = distance
pull_dim            = Y Y Y
pull_ngroups        = 1
;pull_group0         =
pull_group1         = peptide_A
pull_k1             = 500
pull_init1          = 0.00

nsteps              =  250000             ; REMOVE_FOR_EM
tinit               =  49000              ; REMOVE_FOR_EM
dt                  =  0.004              ; REMOVE_FOR_EM
nstxout             =  250000             ; REMOVE_FOR_EM
nstvout             =  250000             ; REMOVE_FOR_EM
nstfout             =  250000             ; REMOVE_FOR_EM
nstenergy           =  25000     ; REMOVE_FOR_EM
nstxtcout           =  25000     ; REMOVE_FOR_EM
nstlog              =  250000    ; REMOVE_FOR_EM
gen_vel             =  no
unconstrained-start =  yes

integrator          =  sd
gen_seed            =  -1
comm_mode           =  linear
nstcomm             =  1
comm_grps           =  System
nstlist             =  5
ns_type             =  grid
pbc                 =  xyz
coulombtype         =  PME
rcoulomb            =  0.9
fourierspacing      =  0.12
pme_order           =  4
vdwtype             =  cut-off
rvdw_switch         =  0
rvdw                =  1.4
rlist               =  0.9
DispCorr            =  EnerPres
Pcoupl              =  Berendsen          ; REMOVE_FOR_EM
pcoupltype          =  isotropic          ; REMOVE_FOR_EM
compressibility     =  4.5e-5             ; REMOVE_FOR_EM
ref_p               =  1.                 ; REMOVE_FOR_EM
tau_p               =  4.0                ; REMOVE_FOR_EM
tc_grps             =  System             ; REMOVE_FOR_EM
tau_t               =  1.0                ; REMOVE_FOR_EM
ld_seed             =  -1                 ; REMOVE_FOR_EM
ref_t               =  300.               ; REMOVE_FOR_EM
gen_temp            =  300.               ; REMOVE_FOR_EM
constraints         =  all-bonds          ; REMOVE_FOR_EM
constraint_algorithm=  lincs              ; REMOVE_FOR_EM
lincs-iter          =  1                  ; REMOVE_FOR_EM
lincs-order         =  6                  ; REMOVE_FOR_EM