[gmx-users] minimum distance between the protein and its mirror image

[Justin Lemkul]

On 8/29/16 5:02 AM, YanhuaOuyang wrote:
> Hi,
>    I am running a REMD of a disordered protein, I visualized the trajectory in VMD and I found that the protein is very close to the box edge.
>    Then I use "gmx mindist " to  check  if a protein has seen its periodic image during simulation. When I used the command "gmx mindist -f remd_01.pdb -s remd.tpr -od mindist.xvg -pi" I choose the 1 group---protein. I choose some data from  mindist.xvg, they are as follow:
>         0        2.800  5.225  7.200  7.200  7.200
>         2        2.793  5.136  7.200  7.200  7.200
>         4        2.804  5.002  7.200  7.200  7.200
>         6        2.777  5.176  7.200  7.200  7.200
>         8        2.820  5.187  7.200  7.200  7.200
>         10       2.871  5.043  7.200  7.200  7.200
>         12       2.788  5.089  7.200  7.200  7.200
>         14       2.882  4.892  7.200  7.200  7.200
>        ................
>         5154     4.153  3.415  7.200  7.200  7.200
>         5156     4.222  3.483  7.200  7.200  7.200
>         5158     4.154  3.608  7.200  7.200  7.200
>         5172     3.607  4.124  7.200  7.200  7.200
>         5174     3.556  4.140  7.200  7.200  7.200
>         5176     3.303  4.430  7.200  7.200  7.200
>         5178     3.291  4.297  7.200  7.200  7.200
>         ...................
>         5880     1.659  5.595  7.200  7.200  7.200
>         5882     1.787  5.564  7.200  7.200  7.200
>         5884     1.718  5.575  7.200  7.200  7.200
>         5886     1.669  5.654  7.200  7.200  7.200
>         5888     1.636  5.752  7.200  7.200  7.200
>         5890     1.590  5.761  7.200  7.200  7.200
>         5892     1.620  5.786  7.200  7.200  7.200
>         5894     1.513  5.791  7.200  7.200  7.200
>         5896     1.523  5.908  7.200  7.200  7.200
> I set the short-range VDW and electrostatic cutoffs=1.0 nm, the distance between the outside of protein and the edge of box is 1.0 nm. the Minimum distance to periodic image ranges from 1.5 nm to 4.2 nm from the data above. While the deal value should be at least 2.0 nm, which is double the cutoff.
> Do anyone knows the simulation is normal and if a protein has seen its periodic image during simulation?

It has not seen its periodic image with cutoffs = 1.0 nm.  You have a very thin 
shell of water around the protein, though, which means there could be some 
artificial ordering, but whether or not that's enough to seriously perturb the 
dynamics is not immediately clear.

> which group should I choose when i using gmx mindist, protein, C-alpha or some else?
>

Protein.  You need to verify that all protein atoms behaved correctly.  CA atoms 
are unlikely to ever see their own periodic images unless you have done 
something horribly wrong in setting up your box.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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