[gmx-users] Umbrella sampling PMF, drug and membrane with pull_geometry=cylinder

Justin A. Lemkul jalemkul at vt.edu
Sun Apr 29 17:15:16 CEST 2012

On 4/29/12 4:46 AM, J B wrote:
>  > Is the problem specific to cylinder geometry? Do other settings work? Does it
>  > make a difference if you set values for pull_r0 and pull_r1?
>  >
>  > -Justin
> I would think that it is the cylinder geometry that creates the problem.
> If I use
> pull = umbrella
> pull_geometry = distance
> pull_dim = N N Y
> pull_start = yes
> pull_init1= 0.0
> pull_ngroups = 1
> pull_group0 = DPPC
> pull_group1 = drug
> pull_rate1 = 0.0
> The molecules stays in place. But pull_geometry=distance is what I would prefer
> due to the undulations.
> Changing pull_r0 and pull_r1 still makes the drug molecule move down towards the
> membrane...

Does the cylinder geometry work if you use "pull_start = no" and pull_init1 
equal to your starting (restraint) distance?  I'm just trying to go through all 
of the iterations of what might be failing.  In theory, what you're doing is 
fine but I'd be interested to know if there was something failing in the input 
parsing such that pull_start is not being properly applied.  The screen output 
of grompp will also tell you what it believes the restraint distance is.  If it 
prints 0, then there's a problem with input processing.

If the problem is reproducible in the latest Gromacs version (4.5.5), please 
file a bug report on redmine.gromacs.org so that it can be investigated.  Please 
provide .tpr file of the system so that the developers can run what you are 
trying to do and see.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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