On 13/04/2011 2:10 AM, Anna Duncan wrote:
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
This looks like a standard case of
http://www.gromacs.org/Documentation/Terminology/Blowing_Up, which can
be quite situation dependent. In the absence of further information, I'd
guess that 4.0 got lucky with the numerical integration, and 4.5.4 didn't.
########################################################################
I've run g_gmxdump/gmxdump to get the input parameters for the
simulations using the 2 different versions,
gmxcheck is a good tool for comparing various file types.
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
The heuristics by which these are set by default have changed. These
values are not of themselves indicative of a problem.
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
These only matter if you're using the relevant algorithms, for which the
defaults have apparently changed.
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)}
Since I don't think any native 4.0 forcefield used CMAP at all, I infer
you aren't, so this doesn't matter either.
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?
We don't know whether you're even using T-coupling, P-coupling or CMAP.
How about a quick description of your objective, simulation system,
equilibration protocol and maybe an .mdp file?
In any case, until you've exhausted the diagnosis steps on the above
link, the smart money is betting that you have a somewhat unhappy
starting configuration.
Mark
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