, May I also Know if they can be uniformly distributed in the
water after solvation?
Thank you very much
Best regards
Meisam
> meisam valizadeh kiamahalleh wrote:
> > Dear GMX users
> > Good day to you
> > I have some drug molecules (cisplatin) added manually and
> > ran
Dear GMX users
Good day to you
I have some drug molecules (cisplatin) added manually and randomly inside a
system which is going to be solvated in spc216 water. I used genbox command
to add the correct number of water molecules needed to solvate the box. The
drug molecules are located very closed
e-ID: <4e820a2e.30...@vt.edu>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
>
>
> meisam valizadeh kiamahalleh wrote:
> > Dear Marcelo
> >
> > Thank you very much for you kind reply.
> > Actually, I am following Justin Lemuk's tutoria
in Lemkul's tutorial. It's very well explained step by
> step:
>
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/index.html
> Good luck,
> Marcelo
>
> On Tue, Sep 27, 2011 at 10:49 AM, meisam valizadeh kiamahalleh <
> meisam.
Dear GMX Users
I would like to let you know that I have run MD simulation on a Carbon
nanotube- drug system.
All steps (Energy minimization, Postion restrained, Equilibration with NVT
and NPT ensembles and finally MD) have been done successfully. Currently if
would like to calculate binding free
Dear Gmx users
I have run MD on carbon nanotube with solvated drug molecules inside and
outside the tubes. Kindly would you please let me know how I
can visualize and calculate the amount of molecules only inside the carbon
nanotube during MD process. May I know what keywords I should use in graph
Dear Gmx users
I have run MD on carbon nanotube with solvated drug molecules inside and
outside the tubes. Kindly would you please let me know how I
can visualize and calculate the amount of molecules only inside the carbon
nanotube during MD process. May I know what keywords I should use in graph
bject: Re: [gmx-users] Re: Warning and Notes in Grompp for
>minimization
> To: Discussion list for GROMACS users
> Message-ID: <4e50b493.3050...@anu.edu.au>
> Content-Type: text/plain; charset="iso-8859-1"
>
> On 21/08/2011 4:42 PM, meisam valizadeh kiamahalle
;
> Subject: Re: [gmx-users] Warning and Notes in Grompp for minimization
> To: Discussion list for GROMACS users
> Message-ID: <4e502903.6010...@vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> meisam valizadeh kiamahalleh wrote:
> >
Dear gmx-users
Good day to you
I have a system including carbon nanotube (1260atoms) and 18 Cisplatin
molecules (198atoms) =1458atoms. I have created the topology file of the
system and now I would like to run minimization on this system.
The content of my mdp file is as below;
define
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