[gmx-users] Umbrella Sampling - Pulling distance larger 0.49 times box size Error during NPT equilibration

[Chenlin Lu]

Dear gromacs users,


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 pulling 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. The point is the coordinate of Au ion changes significantly and doesn't along the pull direction (the movement direction is vertial with the pull direction). It is supposed to be in a neighbourhood of the specified distance, isn't it? Why would this happen?  Could anybody help me?

Thanks,
Chenlin

--------------------------------------------------

Chenlin Lu

Department of Chemical Engineering, 

Tsinghua University, Beijing, 100084

Tel: 86-13120180517

Email: lucl17 at mails.tsinghua.edu.cn