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