[gmx-users] Re: Poteintial energy of my system

Justin Lemkul jalemkul at vt.edu
Wed Dec 12 14:16:40 CET 2012

On 12/12/12 8:14 AM, Shima Arasteh wrote:
> I write the exact commands up to grompp here, not to miss anything;
> 1. pdb2gmx -f dimer-rotated.pdb -o dimer-processed.pdb -ter -water tip3p
> 2. grompp -f minim.mdp -c md-popc.gro -p topol_popc.top -o em.tpr
> 3. trjconv -s em.tpr -f md-popc.gro -o popc-whole.gro -pbc mol -ur compact
> 4. editconf -f dimer-processed.pdb -o dimer-newbox.pdb -c -box 8.78486   8.51308  12.40746
> 5. editconf -f dimer-newbox.pdb -o dimer-newbox.gro
> 6. cat dimer-newbox.gro popc-whole.gro > system.gro
> 7. genrestr -f dimer-newbox.gro -o strong_posre.itp -fc 100000 100000 100000
> 8. perl inflategro.pl system.gro 6 POPC 14 system_inflated.gro 5 area.dat
> 9. grompp -f minim.mdp -c system_inflated.gro -p topol.top -o em.tpr
> 10. mdrun -deffnm em
> The positive potential I have got here, is before the "solvate with water step". I don't have sol molecules in my .top file, however I see sol molecules in system.gro . I visualized system_inflated.gro , I don't see any water molecules.
> Now, I'm confused if this potential energy of a system with sol molecules or these are just droplets as you said?

Your results are fine.  InflateGRO removes water molecules (as stated in its 
documentation).  You should only be concerned if the potential energy of the 
final system (with water and ions, after all the rounds of shrinking are done) 
is positive.  The energies of these intermediate steps mean very little.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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