[gmx-users] re:Membrane Peptide+ DPPC+ Water simulation

[pandey at bioinfo.ernet.in]

Hi Group,

Thanks to John Shims, I have been able to run grompp command with modified
ffgmxnb.itp and ffgmxbon.itp

But, as usual I am again getting error while grompp in shuffle mode, it is
get terminated with "segmentation fault"

I am running with following commands:
------------------------------------------------------
grompp -np  8 -shuffle -sort -f em.mdp -c cla_b4ion.gro -p cla_1.top -o
b4em.tpr;
mdrun_mpi -np 8 -shuffle -sort  -s b4em.tpr -c minimized_cla.gro -o
minimized_cla.trr -e
------------------------------------------------------------

----------------error msg-----------------------------------
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1#
Warning: as of GMX v 2.0 unit of compressibility is truly 1/bar
checking input for internal consistency...
Generated 682 of the 1830 non-bonded parameter combinations
Excluding 3 bonded neighbours for Protein_A 1
Excluding 3 bonded neighbours for DPPC 13
Excluding 2 bonded neighbours for SOL 1295
Excluding 1 bonded neighbours for Cl 1
..........
Sorting coordinates for    13 copies of molecule DPPC
Sorting coordinates for     1 copies of molecule Protein_A
Sorting coordinates for  1295 copies of molecule SOL
Sorting coordinates for     1 copies of molecule Cl
double-checking input for internal consistency...
renumbering atomtypes...
converting bonded parameters...
WARNING 1 [file "cla_1.top", line 1611]:
  atom Cl (Res Cl-228) has mass 0

Reading file b4em.tpr, VERSION 3.1.4 (single precision)
Reading file b4em.tpr, VERSION 3.1.4 (single precision)
Steepest Descents:
   Tolerance         =  1.00000e+03
   Number of steps   =         1000
ERROR: 0031-250  task 0: Segmentation fault
ERROR: 0031-250  task 25: Terminated
--------------------section of *.top  file----------------------
; Include forcefield parameters
#include "/home/others/indira/lyso/wet/lipid/ffG43a2x/ffG43a2x.itp"
#include "/home/others/indira/lyso/wet/lipid/dppc.itp"
#include "ions.itp"

[ moleculetype ]
; Name            nrexcl
Protein_A           3

[ atoms ]
[.......]

;  i funct       fcx        fcy        fcz
   1    1       1000       1000       1000
#endif
[ moleculetype ]
; molname   nrexcl
CL-     1

[ atoms ]
; id    at type res nr  residu name at name  cg nr  charge   mass
1   CL- 1   CL-     CL   1  -1   35.45300

#endif

[ system ]
; Name
Protein in water

[ molecules ]
; Compound        #mols
Protein_A           1
DPPC               13
SOL              1295
Cl 		    1

--------------------------------------
md.mdp file
--------------------------------------
title           = cla
cpp             = /usr/local/bin/cpp; the c pre-processor
constraints     = all-bonds
integrator      = md
dt              = 0.002 ; ps !
nsteps          = 25000 ; total 50 ps.
nstcomm         = 1
nstxout         = 2500 ; collect data every 1 ps
nstvout         = 0
nstfout         = 0
nstlist         = 10
ns_type         = grid
rlist           = 0.9
coulombtype     = PME
rcoulomb        = 0.9
rvdw            = 0.9
fourierspacing  = 0.12
fourier_nx      = 0
fourier_ny      = 0
fourier_nz      = 0
pme_order       = 4
ewald_rtol      = 1e-5
optimize_fft    = yes
; Berendsen temperature coupling is on in two groups
Tcoupl          = berendsen
tau_t           = 0.1 0.1 0.1 0.1
tc-grps         = protein DPPC sol Cl
ref_t           = 300 300 300 300
; Pressure coupling is on
Pcoupl          = berendsen
pcoupltype      = isotropic
tau_p           = 0.5
compressibility = 4.5e-5
ref_p           = 1.0
; Generate velocites is on at 300 K.
gen_vel         = yes
gen_temp        = 300.0
gen_seed        = 173529
------------------------------------------------------

Any help would be greatly appreciated

Thanks and Regards

Om Prakash
Bioinformatcs Center
University of Pune
Pune
India


> Hi,
> The reason why you are getting the atomtype LC3 error is that there is
> another file on Peter Tielemans web site called lipid.itp that you need to
> include into the non-bonding file which corresponds to the forcefield you
> are using (ie ffG43a2xnb.itp). The dppc.itp file refers to parameters
> within
> the lipid itself (bond length, angle, charges etc). All that you do is cut
> and paste the corresponding entries from the lipid.itp file into the
> correct
> non-bonding file. Another thing is that there is also a GROMOS9645a3 also
> with improved aliphatic hydrocarbon parameters. I havent look at this yet,
> but you may want to.
> Cheers
> John
>
>
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
>