[gmx-users] Pull-code implementation Gromacs_v5.0.2

raghav singh raghavbioinfo at gmail.com
Thu Apr 2 19:40:11 CEST 2015

Dear All,

I have a small ssDNA and I am trying to pull one end of strand while
restraining the other end.
As I have previously used the SMD method in gromacs and it worked perfectly
for me but this time with the current version; when I am applying the same
set-up both the ends of single strand are moving along the same axis. The
fixed atom should not be moving (except minor fluctuations).

here are my pull-code parameters

; Pull code
pull             = umbrella
pull-geometry   = distance  ; simple distance increase
pull-dim         = Y N N
pull-start       = yes       ; define initial COM distance > 0
*pull-ngroups   = 1*
*pull-ncoords     = 1*
*pull-coord1-groups    = 0 1   (absolute reference problem); *
*                                           = 1 2   (both ends are moving);
*(could someone please explain it to (I have already read Justin's
explanation but it is still not clear to me))*
pull-group0-name           = Res_A ; Fixed group
pull-group1-name            = Res_B ; SMD group
pull-coord1-rate       = 0.001      ; 0.001 nm per ps = 1 nm per ns
pull-coord1-k         = 1000      ; kJ mol^-1 nm^-2

I am continuing from the NPT equilibration simulation and even after
tinkering with parameters and reading the user list answers; I am still not
able to implement the pull code as it is supposed to be.

Please, help me out in understanding what is wrong with this set-up.

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