[gmx-users] Simulation of membrane protein

[James Starlight]

Dear Justin,

After 20 iterations I've obtained structure like this
http://www.sendspace.com/file/gyyj38


I suppose that this variat is more closely to correct form :)

But during solvation via GenBox I've obtained that error

One of the box vectors has become shorter than twice the cut-off length or
box_yy-|box_zy| or box_zz has become smaller than the cut-off.

Where I can change that cut-off distance?


James


2011/10/17 Justin A. Lemkul <jalemkul at vt.edu>

>
>
> James Starlight wrote:
>
>> Ok, James thank you
>>
>> It seems that I should to wite some script for too many iterations e.g
>>
>> perl inflategro.pl <http://inflategro.pl> minimized1.gro 0.95 DPPC 0
>> shrinked1.gro 5 area_shrink1.dat
>>
>>
>> grompp -f minim.mdp -c shrinked1.gro -p topol.top -o minimized2.tpr
>>
>> mdrun -v -deffnm minimized2
>>
>> perl inflategro.pl <http://inflategro.pl> minimized2.gro 0.95 DPPC 0
>> shrinked2.gro 5 area_shrink1.dat
>>
>>
>> grompp -f minim.mdp -c shrinked2.gro -p topol.top -o minimized3.tpr
>>
>> mdrun -v -deffnm minimized2
>>
>> ......
>>
>> perl inflategro.pl <http://inflategro.pl> minimized20.gro 0.95 DPPC 0
>> shrinked20.gro 5 area_shrink1.dat
>>
>>
>> grompp -f minim.mdp -c shrinked20.gro -p topol.top -o minimized21.tpr
>>
>> mdrun -v -deffnm minimized21
>>
>>
> All of which can be done in a for-loop instead of typing it out manually.
>
>
>  Does this action sequence correct? So as the consequence I need to find
>> operator wich stop the script untill defined value of S per lipid will be
>> reached
>>
>>
> Yes.  You can read that value from the screen or from the area.dat file
> that inflategro.pl prints.
>
>
> -Justin
>
> --
> ==============================**==========
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==============================**==========
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
> Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20111017/b31366b8/attachment.html>