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

[Chenlin Lu]

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

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Chenlin Lu

Department of Chemical Engineering, 

Tsinghua University, Beijing, 100084

Tel: 86-13120180517

Email: lucl17 at mails.tsinghua.edu.cn