[gmx-users] solvation
Jamie Seyed
jamie.seyed at gmail.com
Thu Aug 13 20:39:44 CEST 2009
Hi Justin,
Does it mean each time I can add one until I get the number that I want...??
Many Thanks/Jamie
On Thu, Aug 13, 2009 at 2:13 PM, Justin A. Lemkul <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>> 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
>
> ========================================
> _______________________________________________
> gmx-users mailing list gmx-users at gromacs.org
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> Please search the archive at http://www.gromacs.org/search before posting!
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