[gmx-users] Segmentation Fault in EM

[Justin A. Lemkul]

TJ Mustard wrote:
> 
> 
>  
> 
> On January 17, 2011 at 1:20 PM "Justin A. Lemkul" <jalemkul at vt.edu> wrote:
> 
>  >
>  >
>  > TJ Mustard wrote:
>  > >
>  > >
>  > > Hi all,
>  > >
>  > > 
>  > >
>  > > I have been running alot of simulations on protein ligand interactions,
>  > > and my settings/setup/mdp files worked great for one system. Then when
>  > > we moved to a larger and more complicated system we started getting
>  > > mdrun segmentation faults during "steep" energy minimization.  This
>  > > happens on our cluster and on our iMacs.
>  > >
>  > > 
>  > >
>  > > Any help would be appreciated. Also I can attach my mdp files.
>  > >
>  > > 
>  >
>  > There are a whole host of things that could be going wrong.  Without
>  > substantially more information, including even more (like a thorough 
> description
>  > of what these systems are and the exact commands of what worked 
> before), then
>  > you won't get any useful advice.
>  >
>  > -Justin
>  >
> 
> Ok, system 1 that worked is biotin and strepavidin in a water box, and 
> the "larger" system is just rifampicin in a water box for hydration 
> energies. Both ligands are being removed via FEP.
> 
>  
> 
> As for commands they are identical as we have made a systematic script 
> that sets up our systems.
> 
>  
> 
> It is:
> 
>  
> 
> 
> pdb2gmx -f base.pdb -o base.gro -p base.top
> 
>  
> 
> ===Here we put the ligand .gro and the protein "base" .gro together.
> 
>  
> 
> editconf -bt cubic -f base.gro -o base.gro -c -d 3.5
> 
> genbox -cp base.gro -cs spc216.gro -o base_b4ion.gro -p base.top
> 
> 
> grompp -f em.mdp -c base_b4ion.gro -p base.top -o base_b4ion.tpr -maxwarn 2
> 
> genion -s base_b4ion.tpr -o base_b4em.gro -neutral -conc 0.01 -pname NA 
> -nname CL -g base_ion.log -p base.top
> 
>  
> 
> ==Here select SOL
> 
>  
> 
> grompp -f em.mdp -c base_b4em.gro -p base.top -o base_em.tpr
> 
> mdrun -v -s base_em.tpr -c base_after_em.gro -g emlog.log -cpo stat_em.cpt
> 
>  
> 
> ===Segmentation fault occurs here.
> 
> 
> grompp -f pr.mdp -c base_after_em.gro -p base.top -o base_pr.tpr
> 
> mdrun -v -s base_pr.tpr -e pr.edr -c base_after_pr.gro -g prlog.log -cpi 
> state_pr.cpt -cpo state_pr.cpt -dhdl dhdl-pr.xvg
> 
> grompp -f md.mdp -c base_after_pr.gro -p base.top -o base_md.tpr
> 
> mdrun -v -s base_md.tpr -o base_md.trr -c base_after_md.gro -g md.log -e 
> md.edr -cpi state_md.cpt -cpo state_md.cpt -dhdl dhdl-md.xvg
> 
> grompp -f FEP.mdp -c base_after_md.gro -p base.top -o base_fep.tpr
> 
> mdrun -v -s base_fep.tpr -o base_fep.trr -c base_after_fep.gro -g 
> fep.log -e fep.edr -cpi state_fep.cpt -cpo state_fep.cpt -dhdl dhdl-fep.xvg
> 
>  
> 
> I can include mdp files if that would help.
> 

Yes, please do.

-Justin

>  
> 
> Thank you,
> 
> TJ Mustard
> 
>  
> 
>  
> 
>  > >
>  > > Thank you
>  > >
>  > > 
>  > >
>  > > TJ Mustard
>  > > Email: mustardt at onid.orst.edu
>  > >
>  >
>  > --
>  > ========================================
>  >
>  > Justin A. Lemkul
>  > Ph.D. Candidate
>  > ICTAS Doctoral Scholar
>  > MILES-IGERT Trainee
>  > Department of Biochemistry
>  > Virginia Tech
>  > Blacksburg, VA
>  > jalemkul[at]vt.edu | (540) 231-9080
>  > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>  >
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>  >
> 
>  
> 
> TJ Mustard
> Email: mustardt at onid.orst.edu
> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================