[gmx-users] choosing box vectors
gromacsquery at gmail.com
Sat Jun 15 02:08:28 CEST 2013
I saw your tutorial (
But my case is different. I can not even generate tpr file (trjconv as
tutorial says) as it need box info
Can you please suggest what can be the best possible way? If I just use
system size dimension (X, Y Z) and do mimization it break my system in
How to choose optimum box vector in such case?
On Sat, Jun 15, 2013 at 2:49 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
> On 6/14/13 7:37 PM, gromacs query wrote:
>> Dear Justin,
>> Thanks for reply. Yes sorry indeed its taking box vector from pdb (which I
>> dont want to use as I think they are wrong). In my case if I have already
>> water molecules in my system then if I use:
>> editconf -f del.pdb -o del.gro -c -d 0.0 -bt cubic
>> even now also I see pbc box (in vmd) its quite big than system as you can
>> see from output
>> system size : 10.707 11.077 7.493 (nm)
>> diameter : 14.737 (nm)
>> center : 6.928 6.932 6.936 (nm)
>> box vectors : 0.000 0.000 0.000 (nm)
>> box angles : 0.00 0.00 0.00 (degrees)
>> box volume : 0.00 (nm^3)
>> shift : 0.441 0.436 0.432 (nm)
>> new center : 7.369 7.369 7.369 (nm)
>> new box vectors : 14.737 14.737 14.737 (nm)
>> new box angles : 90.00 90.00 90.00 (degrees)
>> new box volume :3200.60 (nm^3)
>> What should I do?
> You're specifying a cubic box, but for most membrane systems, that's
> probably wrong. What editconf is doing is determining what box vectors are
> necessary, then since you're telling it to make the box cubic, it's forcing
> all of the vectors to be the same. Apparently you have at least one
> dimension that, in this case, is 14.737 nm in length, and then all other
> vectors are then set to the same value.
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
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