[gmx-users] EM in kalp15_DPPC
shima_arasteh2001 at yahoo.com
Tue Aug 21 12:35:51 CEST 2012
Allright, I will check the configurations of out and inputs to find out the reason of warning.
Please let me know something:
Should I expect to see changes in area per lipids in each shrinking or it would happen after 25th repeat suddenly?
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: Tuesday, August 21, 2012 2:57 PM
Subject: Re: [gmx-users] EM in kalp15_DPPC
On 8/21/12 6:14 AM, Shima Arasteh wrote:
> I'm doing the KALP-15 IN DPPC through the Justin's tutorial http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/03_solvate.html
> The problem I got stuck into, is in "2. Pack the lipids around the protein" step.
> After generating the new position restrain file, I start to energy minimization to get the correct area per lipid. As below:
> Scale the lipid positions by a factor of 4:
> #perl inflategro.pl system.gro 4 DPPC 14 system_inflated.gro 5 area.dat
> LOOP :
> Energy minimization with restrained protein
> #grompp -f minim.mdp -c system_inflated.gro -p topol.top -o em.tpr -maxwarn 1
Why are you using -maxwarn? It's almost always a bad idea. What error are you
trying to circumvent?
> #mdrun -deffnm em
> scale down the lipids by a factor of 0.95
> #perl inflategro.pl em.gro 0.95 DPPC 0 system_shrink1.gro 5 area_shrink1.dat
> The EM contains a warning:
> Tolerance (Fmax) = 1.00000e+03
> Number of steps = 50000
> Warning: 1-4 interaction between 2321 and 2325 at distance 2.307 which is larger than the 1-4 table size 2.200 nm
> These are ignored for the rest of the simulation
> This usually means your system is exploding,
> if not, you should increase table-extension in your mdp file
> or with user tables increase the table size
> but because of the -maxwarn 1 its output is:
> Steepest Descents converged to Fmax < 1000 in 557 steps
> Potential Energy = -9.2383398e+04
> Maximum force = 9.0041455e+02 on atom 65
> Norm of force = 7.1919853e+01
> First, is it acceptable to ignore that warning?
Generally not. You should check your input and output configurations carefully.
Something is wrong.
> # perl inflategro.pl em.gro 0.95 DPPC 0 system_shrink1.gro 5 area_shrink1.dat
> Determining upper and lower leaflet...
> 66 lipids in the upper...
> 62 lipids in the lower leaflet
> Centering protein....
> Writing scaled bilayer & centered protein...
> Calculating Area per lipid...
> Protein X-min/max: 122 136
> Protein Y-min/max: 122 135
> X-range: 14 A Y-range: 13 A
> Building 14 X 13 2D grid on protein coordinates...
> Calculating area occupied by protein..
> full TMD..
> upper TMD....
> lower TMD....
> Area per protein: 2 nm^2
> Area per lipid: 9.29991419025 nm^2
> Area per protein, upper half: 1.75 nm^2
> Area per lipid, upper leaflet : 9.02188648751515 nm^2
> Area per protein, lower half: 2 nm^2
> Area per lipid, lower leaflet : 9.59991142219355 nm^2
> Writing Area per lipid...
> Here, the area per lipid is too far from 71 Å2!
Then you haven't done enough iterations of shrinking. The outcome from 26
iterations of shrinking is very reproducible.
Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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