[gmx-users] solvation
Justin A. Lemkul
jalemkul at vt.edu
Thu Aug 13 20:13:36 CEST 2009
Jamie Seyed wrote:
> Hi Justin,
> I made an insert.gro file for 2 water molecules, and when I used genbox
> I got a fatal error: more than one residue in insert molecules, program
> terminated.
Right, like I said before, the insert.gro file should contain coordinates for
*one* molecule.
> I wanted to look at insert.gro, it does not show anything. And when I
> convert it to pdb I got a warning [file aminoacids.dat, line 1]: Bad box
> file insert.gro
Well, how did you make this file? A .gro file has a specific format:
http://manual.gromacs.org/current/online/gro.html
> When I looked at the insert.pdb file I found only 1.5 water molecule!
> Which means 1 water plus a OH. Do you have any idea what should I do or
> if I am missing some thing? Many Thanks in Advance/Jamie
>
I have no idea how you created this broken file, so I can't really comment :)
The easiest thing to do (I would think) would be to take the first molecule of
spc216.gro, keep the header lines, set number of atoms = 3 and preserve the box
information at the bottom. I've used that before in a few cases.
-Justin
> On Thu, Aug 13, 2009 at 1:20 PM, Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> wrote:
>
>
>
> Jamie Seyed wrote:
>
> Hi Justin,
> Thanks for your answer,
> On Thu, Aug 13, 2009 at 11:42 AM, Justin A. Lemkul
> <jalemkul at vt.edu <mailto:jalemkul at vt.edu>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>> wrote:
>
>
>
> Jamie Seyed wrote:
>
> Dear all,
> I want to know how can I use genbox to fill inside of the
> pore
> as well as a layer outside. From the "man genbox" page I
> try to
> use -shell with a negative value (?) but it put waters
> far from
> the outside of the pore and I think it does not care
> about the
> sign. It seems strange to me because when I had 10 10 10
> in the
> last line of my f.gro, by a shell 0.5 or 0.2, I got a
> layer of
> few molecule around the pore, but when I change it to 1.
> 1. 1.,
> the water molecules generated far away. I appreciate if
> someone
> tell me (1) how I can add water inside the pore and (2) why
>
>
> (1) The -vdwd option may help, or even -ci -nmol. If you have a
> pore, wouldn't water diffuse in over time anyway during
> equilibration (assuming an otherwise correct setup and realistic
> physical model)?
>
> Long time ago I did an experiment on water in confined geometry
> and I want to see if the results can obtain from the
> simulation... So for using -nmol -ci (at random position), it
> says I must use a file like insert.gro would you please explain
> me how I can make insert.gro?
>
>
> The "insert.gro" file contains the coordinates of one molecule that
> you want to insert, i.e. one water molecule.
>
> -Justin
>
> (2) If you haven't re-positioned your system within the box, it
> probably doesn't make any sense. The Gromacs convention is
> to place
> the corner of the box at the coordinate origin, and
> everything else
> is relative to that. Is a 1-nm cubic box large enough to
> encompass
> your system? If not, genbox is doing what it's told - filling a
> 1-nm box near the origin, and leaving everything else out.
>
>
>
> -Justin
>
> changing the box size will give a opposite result. Please
> advise..Thanks in advance/Jamie
>
>
>
> ------------------------------------------------------------------------
>
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> -- ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu/> <http://vt.edu/> | (540)
> 231-9080
>
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu/> | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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