[gmx-users] Re: GPCR MD Tutorial Using GROMACS (URL)

Justin A. Lemkul jalemkul at vt.edu
Fri Apr 27 13:29:35 CEST 2012

On 4/27/12 6:40 AM, Bala S wrote:
> Thanks for the reply.
> I'm following the tutorial.

Please clarify whether you're using Anirban's or mine.  Now that two exist, 
people will have to be a fair bit more specific :)

> In your system, to solvate it you have the values that was used during the
> protien insertion into the bilayer. Following it, I have used the following
> commandfor my system where the protein is very much smaller than the length
> of the bilayer.
> $ editconf -f shrinked4.gro -o shrinked4_1.gro -box 6.41840 6.44350 6.59650
> $ genbox -cp shrinked4_1.gro -cs -o shrinked4_box.gro -p topol.top

If you have to manipulate the box of any coordinate file produced by InflateGRO, 
whatever you're doing is wrong.  You should not be solvating anything until the 
very last step of the procedure, where your bilayer is of correct size and APL.

> But I could see in the visualizer that SOL molecules were added on top and
> bottom but only 1/3 of the length of the bilayer.
> How to add SOL molecules to whole length or how to remove not-solvated part
> of lipids?

This outcome is a consequence of re-adjusting the box size of a system that 
likely has other dimensions.  As far as I can tell, you shouldn't be doing this.



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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