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
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