[gmx-users] solvation
Jamie Seyed
jamie.seyed at gmail.com
Thu Aug 13 20:52:56 CEST 2009
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
On Thu, Aug 13, 2009 at 2:41 PM, Justin A. Lemkul <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>> 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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