[gmx-users] Fwd: I have a symmetric simulation box,

[Justin Lemkul]

On 10/18/12 6:45 AM, Ali Alizadeh wrote:
> Dear Justin
>
> Please check my commands, Are these correct, step by step?
>
> If these are correct then i will start my simulation with longer time,
>
>

I really don't understand why you're invoking pdb2gmx three times.  You should 
only ever need to produce one topology.  You certainly do not need to run 
pdb2gmx after EM.  That makes no sense at all.  I suppose the effect is 
harmless, but confusing.

-Justin

>
> 1- pdb2gmx -f mixture.pdb -o mix -p mix
>
> 2- editconf -f mix.gro -o mix2.pdb   ; for obtain a clean .pdb for
> obtaining clean .gro and clean .top
>
> 3- pdb2gmx -f mix2.pdb -o mix2.gro -p mix2.top
>
>     STEP 1 :  EM
>
> 5- grompp -f minim.mdp -c mix2.gro -p mix2.top -o em.tpr
>
> 6- mdrun -v -deffnm em
>
>
>    STEP 2 : NVT EQUILIBRATION
>
> 7- editconf -f em.gro -o em.pdb   ; to earn em.gro and em.top for next NPT EM
>
> 8- pdb2gmx -f em.pdb -o nvt -p nvt
>
> 9- grompp -f nvt.mdp -c nvt.gro -p nvt.top -o nvt.tpr
>
> 10- mdrun -v -deffnm nvt
>
> 11- g_energy -f nvt.edr
>
> 12- xmgrace  energy.xvg
>
>
> Sincerely
>

-- 
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================