[gmx-users] solvation
Justin A. Lemkul
jalemkul at vt.edu
Thu Aug 13 20:55:10 CEST 2009
Jamie Seyed wrote:
> Hi Justin,
> My aim is to add water inside the pore (I do not care about outside), so
> as you told me I used the first line of spc216.gro and I do not know why
> after the calculations that I posted before it says segmentation fault??
> Thanks in advance/Jamie
>
Is it giving a seg fault when using a proper .gro file? I don't understand what
you're asking about.
The previous seg fault was from an either improperly-formatted or incomplete
.gro file. Having an intact file should not generate a seg fault, unless the
algorithm is failing (which I have seen when molecules simply will not fit in
the space you're trying to squeeze them).
-Justin
> On Thu, Aug 13, 2009 at 2:41 PM, Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> wrote:
>
>
>
> 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>
> <mailto: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>>
> <mailto: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>>>
> <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 <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/>
> <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/>
> <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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