[gmx-users] KALP15 in DPPC: lipid packing: deleting and shrinking lipids: why are the number of lipids not decreasing?

[Thomas Lipscomb]

Dear gmx-users,
I am not confident doing the lipid packing in this tutorial (using Maximin 3 instead of KALP15):
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/03_solvate.html


And my biggest problem is this error (see my hypothesized solution at the end of this email):
number of coordinates in coordinate file (system_shrink1.gro, 6400) does not match topology (topol.top, 17617)


I have been having trouble with the 3 commands that delete and shrink the lipids (see link for my previous question about them):
https://www.mail-archive.com/gromacs.org_gmx-users@maillist.sys.kth.se/msg08003.html


perl must be first because it generates the system_shrink1.gro and area_shrink1.dat
grompp is next becasuse it is "in between" and it needs system_shrink1.gro
mdrun is last

So the order for the 3 commands iteration 1 should be:
perl inflategro.pl confout.gro 0.95 DPPC 0 system_shrink1.gro 5 area_shrink1.dat
/usr/local/gromacs/bin/gmx grompp -f minim.mdp -c system_shrink1.gro -p topol.top -o em.tpr
/usr/local/gromacs/bin/gmx mdrun -s em.tpr -v

The 3 commands iteration 2 are:
perl inflategro.pl system_shrink1.gro 0.95 DPPC 0 system_shrink2.gro 5 area_shrink2.dat
/usr/local/gromacs/bin/gmx grompp -f minim.mdp -c system_shrink1.gro -p topol.top -o em.tpr
/usr/local/gromacs/bin/gmx mdrun -s em.tpr -v

etc (stop at 26th iteration)

These are the errors I get:

STEP 1
perl inflategro.pl confout.gro 0.95 DPPC 0 system_shrink1.gro 5 area_shrink1.dat


There are 128 lipids...
with 50 atoms per lipid..
Determining upper and lower leaflet...
64 lipids in the upper...
64 lipids in the lower leaflet 
No protein coordinates found...
Writing scaled bilayer & centered protein...

STEP 2
/usr/local/gromacs/bin/gmx grompp -f minim.mdp -c system_shrink1.gro -p topol.top -o em.tpr


NOTE 1 [file minim.mdp, line 18]:  minim.mdp did not specify a value for the .mdp option "cutoff-scheme".  Probably it was first intended for use with GROMACS before 4.6. In 4.6,  the Verlet scheme was introduced, but the group scheme was still the  default. The default is now the Verlet scheme, so you will observe  different behaviour.

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1#

NOTE 2 [file minim.mdp]:  With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note  that with the Verlet scheme, nstlist has no effect on the accuracy of  your simulation.

Setting the LD random seed to 3474377125
Generated 23988 of the 24090 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 1
Generated 20813 of the 24090 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
Excluding 3 bonded neighbours molecule type 'DPPC'
Excluding 2 bonded neighbours molecule type 'SOL'

number of coordinates in coordinate file (system_shrink1.gro, 6400) does not match topology (topol.top, 17617)


system_shrink1.gro goes up to:128DPPC

so 128 DPPC * 50 atoms per DPPC = 6400

topol.top has:
[ molecules ]
; Compound        #mols
Protein_chain_A     1
DPPC              125
SOL          3655

SOLUTION?: So do I change topol.top's [ molecules ] to this to make it agree with 6400:
; Compound        #mols

DPPC              128


And then do I change [ molecules ] between every iteration?

I do not understand why DPPC went from 125 to 128 (or maybe 125 was wrong and it really was 128, so 128 is still 128.  Either way the number of DPPC should be decreasing but it is not.).  Do I have to do more iterations before it decreases?
I thought the number of DPPC really was 125 because a previous step:
perl inflategro.pl system.gro 4 DPPC 14 system_inflated.gro 5 area.dat

did this:
Now there are 128 lipids
with 50 atoms per lipid
There are 3 lipids within cut-off range...
1 will be removed from the upper leaflet...
2 will be removed from the lower leaflet...

128 - 3 = 125

Sincerely,
Thomas