[gmx-users] spurious forces while doing pulling simulation

[Justin A. Lemkul]

Amit Choubey wrote:
> Hi all,
> 
> I am trying to do pulling simulation. Following are the pull parameters
> 
> pull = umbrella
> pull_geometry = direction
> pull_vec1 = 0 0 1
> pull_group1 = RNA
> pull_rate1 = 0.01
> pull_k1 = 1000
> pull_start = yes
> 
> Everything works fine until the pull group COM reaches half the box 
> length. The COM position changes by the box length and that causes huge 
> force on the group. What should i do to fix this ? Also i am using NPT 
> coupling.
> 

You have to use a sufficiently large box, otherwise the periodic distance 
becomes the reference distance when this happens.  This has been discussed 
numerous times on the list (hint: there is an archive for a reason!) and in the 
tutorial linked here:

http://www.gromacs.org/Documentation/Tutorials#Pull_Code_and_Umbrella_Sampling

-Justin

> Amit
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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