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

[Jon]

Thanks, Farid

You were right, when I made the bond, I forgot to make sure the charges 
were all balanced. Thanks for your help.

Cheers
Jon

> From: "Farid Sa'adedin" <fsaadedi at staffmail.ed.ac.uk>
> Subject: Re: [gmx-users] Segmentation fault in genion for
> monolayer-protein system
> 
> Dear Jon
> Something is missing from the pdb as your charges are not do not seem to
> add up correctly. For GROMACS to work the initial charge should be a
> whole number. Double check the pdb to see if anything is missing. If not
> just add charges to your pdb to make it into a whole number. Then you
> can use genion to balance your system.
> 
> Farid
> 
> Quoting Jon <jon.ellis at utoronto.ca>:
>> 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
>> nm2). 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