[gmx-users] Pulled group moves randomly while doing umbrella sampling

[Shayna Hilburg]

That error is solved by switching to *pull_coord1_geometry =
direction-periodic* to let it move over periodic boundary conditions as
described here: http://manual.gromacs.org/online/mdp_opt.html#pull


On Sat, Jun 30, 2018 at 12:07 AM Chenlin Lu <lucl13 at 163.com> wrote:

> Hello,
>
>
> I am doing umbrella sampling to calculate the PMF puling an Au ion out of
> a protein channel. Basically, I followed the procedure given by Justin's
> tutorial. The configuration generation was finished correctly and the .mdp
> file summary_distance.txt are shown below:
>
>
> pull                    = yes
> pull_ngroups            = 2
> pull_ncoords            = 1
> pull_group1_name        = Protein
> pull_group2_name        = AU
> pull_coord1_type        = umbrella      ; harmonic biasing force
> pull_coord1_geometry    = direction      ; simple distance increase
> pull_coord1_groups      = 1 2
> pull_coord1_vec         = 0 0 -1
> pull_coord1_rate        = 0.01
> pull_coord1_k           = 1000          ; kJ mol^-1 nm^-2
> pull_coord1_start       = yes           ; define initial COM distance > 0
> ​
> 0.000 3.220
> 1.000 3.242
> 2.000 3.264
> 3.000 3.354
> 4.000 3.302
> ... ...
> 396.000 0.186
> 397.000 0.175
> 398.000 0.179
> 399.000 0.170
> 400.000 0.185
>
>
> The problem is when I am doing NPT equilibration (the .mdp file is the
> same as before expcet the pull rate is zero) I got a mistake which says
> pull distance is larger than 0.49 times box size. So I checked the
> trajectory which shows the Au ion moves randomly and out of box. Its
> movement doesn't along the pull direction. Why would this happen?
>
>
> Thanks,
> Chenlin
>
> --------------------------------------------------
>
> Chenlin Lu
>
> Department of Chemical Engineering,
>
> Tsinghua University, Beijing, 100084
>
> Tel: 86-13120180517
>
> Email: lucl17 at mails.tsinghua.edu.cn
>
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