[gmx-users] 1-4 ineractions in double precision

[Jessé Nóbrega]

Dear
Gromacs users;

I
have got a problem when performing molecular
dynamics calculations in double precision with Gromacs Version 4.0.7.
My system contains a protein with 482 residues, water molecules and
Cl-ions.  
I
have already carried out this same calculation in single precision
with success.
Below,
I show my output and input files for the calculation in double
precision.
<<<<===============================================================>>>>
starting
mdrun 'Protein in water'  
1000000
steps, 2000.0 ps.  
Warning:
1-4 interaction between 4412 and 4417 at distance inf which is larger
than the 1-4 table size 2.400 nm  
These
are ignored for the rest of the simulation  
This
usually means your system is exploding,  
if
not, you should increase table-extension in your mdp file  
or
with user tables increase the table size  
Warning:
1-4 interaction between 4365 and 4368 at distance inf which is larger
than the 1-4 table size 2.400 nm  
These
are ignored for the rest of the simulation  
This
usually means your system is exploding,  
if
not, you should increase table-extension in your mdp file  
or
with user tables increase the table size  
Warning:
1-4 interaction between 4649 and 4655 at distance inf which is larger
than the 1-4 table size 2.400 nm  
These
are ignored for the rest of the simulation  
Warning:
1-4 interaction between 1336 and 1339 at distance inf which is larger
than the 1-4 table size 2.400 nm  
This
usually means your system is exploding,  
if
not, you should increase table-extension in your mdp file  
or
with user tables increase the table size  
These
are ignored for the rest of the simulation  
This
usually means your system is exploding,  
if
not, you should increase table-extension in your mdp file  
or
with user tables increase the table size  
Warning:
1-4 interaction between 1199 and 1211 at distance inf which is larger
than the 1-4 table size 2.400 nm  
These
are ignored for the rest of the simulation  
This
usually means your system is exploding,  
if
not, you should increase table-extension in your mdp file  
or
with user tables increase the table size  
Warning:
1-4 interaction between 525 and 529 at distance inf which is larger
than the 1-4 table size 2.400 nm  
These
are ignored for the rest of the simulation  
This
usually means your system is exploding,  
if
not, you should increase table-extension in your mdp file  
or
with user tables increase the table size  
rank
2 in job 7 slayer_37486 caused collective abort of all ranks  
exit
status of rank 2: killed by signal 9
<<<<===============================================================>>>>

My
mdp file is:

<<<<<==============================================================>>>>
title
: ldtop1  
cpp :
/usr/bin/cpp ; the c processor  
integrator
: md  
dt :
0.002  
nsteps:
1000000  
nstcomm:1  
nstxout:500  
nstvout:500  
nstfout:0  
nstlist:5  
ns_type:grid  
rlist:0.9  
coulombtype:PME  
rcoulomb:0.9  
rvdw:1.4  
table-extension:4.000  
fourierspacing:0.12  
fourier_nx:0  
fourier_ny:0  
fourier_nz:0  
pme_order:14  
ewald_rtol:1e-5  
optimize_fft:yes  
constraint_algorithm:LINCS  
constraints:hbonds  
lincs_order
:6  
;  
;
Berendsen temperature coupling  
;  
Tcoupl
: V-rescale  
tau_t
: 0.1 0.1 0.1  
tc-grps:
protein SOL CL-  
ref_t
: 300 300 300  
;
;
Pressure Coupling  
;
Pcoupl
: berendsen  
pcoupltype:
isotropic  
tau_p
: 0.5  
compressibility
: 4.5e-5  
ref_p
: 1.0  
;
;
Generate velocity  
;
gen_vel:
yes  
gen_temp
: 300.0  
gen_seed
: 173529
<<<<===============================================================>>>>
Any
help would be appreciated, and if you require further information
please let me know.

Thanks
in advance.
Jesse
da Nóbrega


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