[gmx-users] constant force pulling

[Justin Lemkul]

On 7/29/13 2:42 PM, kim2811 wrote:
> Hi,
>
> I am trying to pull/separate a protein dimer by applying constant force in
> my SMD. The dimer has dimension 9 x 8 x 5 nm^3, and I'm trying to pull in
> the y-direction so I have set the box as 12 x 40 x 8 nm^3. I have also set
> my simulation to run for 5 ns. However, after only 251 ps, I got this fatal
> error:
>
>    Distance of pull group 1 (3.958423 nm) is larger than 0.49 times the box
> size (16.314939)
>

This appears to be a minor output bug.  The violation occurs in the z-dimension, 
since 0.49 * 8 = 3.92.

> Can somebody please interpret this error? When I checked the trajectory, the
> protein seems to be inside the box or at least the COM of the dimer is near
> the center of the box, so the protein approaching near the boundary can't be
> the reason for this error. If it can help to clarify, here's my pull code:
>
> ; Pull code
> pull            = constant_force
> pull_geometry   = direction  ; pull in the direction of pull code
> pull_dim        = Y Y Y

Note that pull_dim should be ignored here, you only need pull_vec1.  The code 
should interpret the .mdp contents correctly, though.

-Justin

> pull_start      = yes       ; define initial COM distance > 0
> pull_ngroups    = 1
> pull_group0     = chain_A  ; C-terminal of Protein 1
> pull_group1     = chain_B  ; C-terminal of Protein 2
> pull_k1         = -500      ; kJ mol^-1 nm^-1
> pull_vec1       = 0 1 0
>
> Thank you.
>
>
>
> --
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> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
>

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

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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