Hi,
I've started using version 4.5.4 of gromacs, having previously been
using version 4.0 on an older server.
When I run a simulation on v4.0 everything seems to run fine.
However, when I run the same simulation on v4.5.4, mdrun gives me the
error message:
########################################################################
Making 3D domain decomposition 4 x 3 x 2
starting mdrun 'PROTEIN IN BILAYER'
5000000 steps, 150000.0 ps.
step 0
Step 11 Warning: pressure scaling more than 1%, mu: 1.02292 1.02292
1.0122
Step 11 Warning: pressure scaling more than 1%, mu: 1.02292 1.02292
1.0122
.
.
.
.
Step 11 Warning: pressure scaling more than 1%, mu: 1.02292 1.02292
1.0122
Step 21 Warning: pressure scaling more than 1%, mu: 1.09061 1.09061
1.02015
Step 21 Warning: pressure scaling more than 1%, mu: 1.09061 1.09061
1.02015
.
.
.
Step 21 Warning: pressure scaling more than 1%, mu: 1.09061 1.09061
1.02015
Step 25, time 0.75 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000004, max 0.000015 (between atoms 147 and 148)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
178 179 34.7 0.2600 0.2600 0.2600
Step 28, time 0.84 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 19.241184, max 126.849724 (between atoms 35 and 36)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
Step 28, time 0.84 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 1.739422, max 8.610986 (between atoms 496 and 497)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
45 46 90.0 0.2650 0.5083 0.2650
35 36 90.0 0.3100 39.6334 0.3100
42 43 90.0 0.2600 1.2129 0.2600
45 46 90.0 0.2650 0.5083 0.2650
482 483 90.0 0.2600 0.8649 0.2600
496 497 90.0 0.2700 2.5950 0.2700
496 498 90.0 0.2700 1.4511 0.2700
497 498 90.0 0.2700 2.5822 0.2700
Wrote pdb files with previous and current coordinates
Wrote pdb files with previous and current coordinates
Segmentation fault
########################################################################
I've run g_gmxdump/gmxdump to get the input parameters for the
simulations using the 2 different versions, which I can't attach
because they're too big but which differ in the lines shown below
(v4.0 on the left and v4.5.4 on the right):
nstcomm = 1 | nstcomm
= 10
nstcalcenergy = 1 |
nstcalcenergy = 10
nsttcouple = 1 | nsttcouple
= 10
nstpcouple = 1 | nstpcouple
= 10
rgbradii = 2 | rgbradii
= 1
sa_surface_tension = 2.092 | sa_surface_tension =
2.05016
sc_sigma_min = 0 | sc_sigma_min
= 0.3
nstdhdl = 1 | nstdhdl
= 10
and also for cmap atomtypes values:
in v4.0:
atomtype[ 0]={radius= 0.00000e+00, volume= 0.00000e+00,
gb_radius= 0.00000e+00, surftens=-1.00000e+00, atomnumber= -1, S_hct=
0.00000e+00)}
atomtype[ 1]={radius= 0.00000e+00, volume= 0.00000e+00,
gb_radius= 0.00000e+00, surftens=-1.00000e+00, atomnumber= -1, S_hct=
0.00000e+00)}
atomtype[ 2]={radius= 0.00000e+00, volume= 0.00000e+00,
gb_radius= 0.00000e+00, surftens=-1.00000e+00, atomnumber= -1, S_hct=
0.00000e+00)}
atomtype[ 3]={radius= 0.00000e+00, volume= 0.00000e+00,
gb_radius= 0.00000e+00, surftens=-1.00000e+00, atomnumber= -1, S_hct=
0.00000e+00)}
atomtype[ 4]={radius= 0.00000e+00, volume= 0.00000e+00,
gb_radius= 0.00000e+00, surftens=-1.00000e+00, atomnumber= -1, S_hct=
0.00000e+00)}
atomtype[ 5]={radius= 0.00000e+00, volume= 0.00000e+00,
gb_radius= 0.00000e+00, surftens=-1.00000e+00, atomnumber= -1, S_hct=
0.00000e+00)}
atomtype[ 6]={radius= 0.00000e+00, volume= 0.00000e+00,
gb_radius= 0.00000e+00, surftens=-1.00000e+00, atomnumber= -1, S_hct=
0.00000e+00)}
atomtype[ 7]={radius= 0.00000e+00, volume= 0.00000e+00,
gb_radius= 0.00000e+00, surftens=-1.00000e+00, atomnumber= -1, S_hct=
0.00000e+00)}
atomtype[ 8]={radius= 0.00000e+00, volume= 0.00000e+00,
gb_radius= 0.00000e+00, surftens=-1.00000e+00, atomnumber= -1, S_hct=
0.00000e+00)}
atomtype[ 9]={radius= 0.00000e+00, volume= 0.00000e+00,
gb_radius= 0.00000e+00, surftens=-1.00000e+00, atomnumber= -1, S_hct=
0.00000e+00)}
atomtype[ 10]={radius= 0.00000e+00, volume= 0.00000e+00,
gb_radius= 0.00000e+00, surftens=-1.00000e+00, atomnumber= -1, S_hct=
0.00000e+00)}
atomtype[ 11]={radius= 0.00000e+00, volume= 0.00000e+00,
gb_radius= 0.00000e+00, surftens=-1.00000e+00, atomnumber= -1, S_hct=
0.00000e+00)}
atomtype[ 12]={radius= 0.00000e+00, volume= 0.00000e+00,
gb_radius= 0.00000e+00, surftens=-1.00000e+00, atomnumber= -1, S_hct=
0.00000e+00)}
atomtype[ 13]={radius= 0.00000e+00, volume= 0.00000e+00,
gb_radius= 0.00000e+00, surftens=-1.00000e+00, atomnumber= -1, S_hct=
0.00000e+00)}
atomtype[ 14]={radius= 0.00000e+00, volume= 0.00000e+00,
gb_radius= 0.00000e+00, surftens=-1.00000e+00, atomnumber= -1, S_hct=
0.00000e+00)}
atomtype[ 15]={radius= 0.00000e+00, volume= 0.00000e+00,
gb_radius= 0.00000e+00, surftens=-1.00000e+00, atomnumber= -1, S_hct=
0.00000e+00)}
atomtype[ 16]={radius= 0.00000e+00, volume= 0.00000e+00,
gb_radius= 0.00000e+00, surftens=-1.00000e+00, atomnumber= -1, S_hct=
0.00000e+00)}
atomtype[ 17]={radius= 0.00000e+00, volume= 0.00000e+00,
gb_radius= 0.00000e+00, surftens=-1.00000e+00, atomnumber= -1, S_hct=
0.00000e+00)}
and in v4.1
atomtype[ 0]={radius=-1.00000e+00, volume=-1.00000e+00,
gb_radius=-1.00000e+00, surftens=-1.00000e+00, atomnumber= -1,
S_hct=-1.00000e+00)}
atomtype[ 1]={radius=-1.00000e+00, volume=-1.00000e+00,
gb_radius=-1.00000e+00, surftens=-1.00000e+00, atomnumber= -1,
S_hct=-1.00000e+00)}
atomtype[ 2]={radius=-1.00000e+00, volume=-1.00000e+00,
gb_radius=-1.00000e+00, surftens=-1.00000e+00, atomnumber= -1,
S_hct=-1.00000e+00)}
atomtype[ 3]={radius=-1.00000e+00, volume=-1.00000e+00,
gb_radius=-1.00000e+00, surftens=-1.00000e+00, atomnumber= -1,
S_hct=-1.00000e+00)}
atomtype[ 4]={radius=-1.00000e+00, volume=-1.00000e+00,
gb_radius=-1.00000e+00, surftens=-1.00000e+00, atomnumber= -1,
S_hct=-1.00000e+00)}
atomtype[ 5]={radius=-1.00000e+00, volume=-1.00000e+00,
gb_radius=-1.00000e+00, surftens=-1.00000e+00, atomnumber= -1,
S_hct=-1.00000e+00)}
atomtype[ 6]={radius=-1.00000e+00, volume=-1.00000e+00,
gb_radius=-1.00000e+00, surftens=-1.00000e+00, atomnumber= -1,
S_hct=-1.00000e+00)}
atomtype[ 7]={radius=-1.00000e+00, volume=-1.00000e+00,
gb_radius=-1.00000e+00, surftens=-1.00000e+00, atomnumber= -1,
S_hct=-1.00000e+00)}
atomtype[ 8]={radius=-1.00000e+00, volume=-1.00000e+00,
gb_radius=-1.00000e+00, surftens=-1.00000e+00, atomnumber= -1,
S_hct=-1.00000e+00)}
atomtype[ 9]={radius=-1.00000e+00, volume=-1.00000e+00,
gb_radius=-1.00000e+00, surftens=-1.00000e+00, atomnumber= -1,
S_hct=-1.00000e+00)}
atomtype[ 10]={radius=-1.00000e+00, volume=-1.00000e+00,
gb_radius=-1.00000e+00, surftens=-1.00000e+00, atomnumber= -1,
S_hct=-1.00000e+00)}
atomtype[ 11]={radius=-1.00000e+00, volume=-1.00000e+00,
gb_radius=-1.00000e+00, surftens=-1.00000e+00, atomnumber= -1,
S_hct=-1.00000e+00)}
atomtype[ 12]={radius=-1.00000e+00, volume=-1.00000e+00,
gb_radius=-1.00000e+00, surftens=-1.00000e+00, atomnumber= -1,
S_hct=-1.00000e+00)}
atomtype[ 13]={radius=-1.00000e+00, volume=-1.00000e+00,
gb_radius=-1.00000e+00, surftens=-1.00000e+00, atomnumber= -1,
S_hct=-1.00000e+00)}
atomtype[ 14]={radius=-1.00000e+00, volume=-1.00000e+00,
gb_radius=-1.00000e+00, surftens=-1.00000e+00, atomnumber= -1,
S_hct=-1.00000e+00)}
atomtype[ 15]={radius=-1.00000e+00, volume=-1.00000e+00,
gb_radius=-1.00000e+00, surftens=-1.00000e+00, atomnumber= -1,
S_hct=-1.00000e+00)}
atomtype[ 16]={radius=-1.00000e+00, volume=-1.00000e+00,
gb_radius=-1.00000e+00, surftens=-1.00000e+00, atomnumber= -1,
S_hct=-1.00000e+00)}
atomtype[ 17]={radius=-1.00000e+00, volume=-1.00000e+00,
gb_radius=-1.00000e+00, surftens=-1.00000e+00, atomnumber= -1,
S_hct=-1.00000e+00)}
I haven't set any of these values and I don't understand why the
default values for parameters such as nsttcouple differ by a factor of
10. I know that in v4.5.4 parameters such as nsttcouple are by
default set to be equal to nstlist (which =10 in my simulations) but I
don't understand how the default is being set in v4.0.
The larger nstpcouple default values seem to me like the cause of my
warning messages and eventual crash of the system when run in v4.5.4
but I am also worried that I don't know how the cmap atomtypes values
are being set and how these differences will affect the simulations.
Do you have any pointers?
Many thanks,
Anna
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