[gmx-users] Segmentation fault in genion for monolayer-protein system

Jon jon.ellis at utoronto.ca
Tue Aug 23 19:34:38 CEST 2005

I am trying to do an energy minimization run of a 148-residue protein 
attached to a monolayer of 289 short alkyl chains. The protein is 
attached to the membrane by an amide bond from a lysine to one of the 
alkys near the centre of the layer (which is ~9.1x9.1 nm^2). I minimized 
the monolayer in vacuum, then attached the protein by editing the .gro 
and .top files.

When I run grompp it, it tells me the charge is -2.449600e+01. When I 
run this in vacuum, it does not minimize properly (I get inf for the 
forces after only a few steps. I tried adding spc water and ions, but 
when I run genion, adding 24 NA+, it gives me a segmentation fault 
immeditely. This reoccurs upon re-grompp-ing, rereunning, and rebooting.

Two questions:
1) How many NA+ ions should I add, 24 or 25, for PME to work properly 
(requires charge =~0)

2) Has anybody ever seen a segmentation fault in genion, or have any 
idea what its all about?

Any other suggestions or comments would be welcome.

Here's my em.mdp
title		    =  Energy Minimization of protein on surface
cpp                 =  cpp
constraints         =  none  ; no bond constraints in EM
define              =  -DFLEX_SPC
integrator          =  steep ; steepest descent min to remove bad vdw
dt                  =  0.002 ; ps
nsteps              =  50000   ; no. of steps
nstlist             =  10		
nstenergy           =  2
ns_type             =  grid		
rlist               =  0.9   ; cut-off distance for list
coulombtype         =  PME
rcoulomb            =  0.9   ; cutoff for colomb
rvdw                =  1.0   ; cutoff for vdw interactions
fourierspacing      =  0.12		
fourier_nx          =  0
fourier_ny          =  0
fourier_nz          =  0
pme_order           =  7
ewald_rtol          =  1e-5
optimize_fft        =  yes
gen_vel             =  no
Tcoupl              =  no
Pcoupl              =  no
;	Energy minimizing stuff
emtol               =  1000
emstep              =  0.0001

Jon Ellis
Institute of Biomaterials and Biomedical Engineering/Dept of Chemistry
University of Toronto

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