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

[Justin Lemkul]

On 7/4/18 6:51 AM, Chenlin Lu wrote:
> 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

This is unlikely to be a viable reaction coordinate. Beware copying too 
closely from the tutorial; it has very unique geometry and 
considerations. Likely you're getting "random" movement because the 
chosen biasing potential is ineffectual.

-Justin

> 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
>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
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jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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