[gmx-users] Re: Poteintial energy of my system
shima_arasteh2001 at yahoo.com
Wed Dec 12 14:14:50 CET 2012
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?
----- Original Message -----
From: Justin Lemkul <jalemkul at vt.edu>
To: Shima Arasteh <shima_arasteh2001 at yahoo.com>
Sent: Wednesday, December 12, 2012 4:19 PM
Subject: Re: [gmx-users] Re: Poteintial energy of my system
On 12/12/12 7:46 AM, Shima Arasteh wrote:
> How about it that I get a positive potential energy for a system of only protein and POPC? Makes sense?
If there's no solvent, then the result makes perfect sense - you've essentially
got a droplet in vacuum, but that's different than what you described below.
Without solvent, you have tons of charged groups in the lipid headgroups (and
possibly in the protein too) that have no interaction with solvent, so you have
lots of unsatisfied interactions that otherwise contribute to a negative
potential in the condensed phase.
> Thanks for your explanation.
> ----- Original Message -----
> From: Justin Lemkul <jalemkul at vt.edu>
> To: Shima Arasteh <shima_arasteh2001 at yahoo.com>; Discussion list for GROMACS users <gmx-users at gromacs.org>
> Sent: Wednesday, December 12, 2012 4:11 PM
> Subject: Re: [gmx-users] Re: Poteintial energy of my system
> On 12/12/12 5:16 AM, Shima Arasteh wrote:
>> What are the possible solutions to solve the problem?
>> My system is composed of protein, POPC, ions, and water. I follow the approached suggested in kalp15-DPPC tutorial.
>> And I got such an incorrect potential for the first grompp.
>> Would you please guide me?
>> I would appreciate ur suggestions.
> The outcome is rather puzzling. Fmax indicates the system should be happy, but the potential is clearly not. A positive potential indicates net repulsion and/or unsatisfied interactions, which should not happen for a condensed phase system. In vacuo, positive potentials are more common (depending, of course, on what the system is). Check for voids in the unit cell. That's about the only thing I can think of.
> -- ========================================
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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