[gmx-users] solvation
Justin A. Lemkul
jalemkul at vt.edu
Thu Aug 13 20:41:02 CEST 2009
Jamie Seyed wrote:
> Hi Justin,
> Does it mean each time I can add one until I get the number that I
> want...?? Many Thanks/Jamie
>
No need to do it manually. That's what -nmol is for.
-Justin
> On Thu, Aug 13, 2009 at 2:13 PM, Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> wrote:
>
>
>
> 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>
> <mailto: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>>
> <mailto: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/>
> <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/> <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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