Hi,<div><br></div><div>I don't see any immediate problem in your file, except the fact that you have to couple all molecule to a heat bath. Second, has much as I know, you can't reach 0K, so what the meaning?</div>
<div><br></div><div>Best,</div><div>Itamar<br><div><br><div class="gmail_quote">On Tue, Jun 2, 2009 at 9:11 PM, Inon Sharony <span dir="ltr"><<a href="mailto:InonShar@tau.ac.il">InonShar@tau.ac.il</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div>
<p>
Hi everyone!
</p>
<p>
I'm trying to run a simulation of a single diatomic Sulfur molecule. When I run an equilibration scheme (generating velocities from a 300K Maxwell-Boltzmann distribution) it runs fine, but when I take the equilibrated molecule and couple one atom to a 0K heat bath (using Stochastic Dynamics) the simulation segfaults at the first step.
</p>
<p>
I've enclosed as much information as I could. Notice (at the very bottom) that the md.log file shows an initial temperature of 17884.7K, but already in the report for step 0 the temperature, as well as many other thermodynamic quantities, are NaN.
</p>
<p>
I've encountered one reference to the same error I'm getting, but itjust said that there was some problem with the input files, but didn'tsay what was the problem...
</p>
<p>
I hope you will find some stupid mistake in the *.mdp file, or something easily remedied...
</p>
<p>
P.S.
</p>
<p>
I know GROMACS is not optimized for simulating tiny molecules, but I don't see why it should be such a critical problem...
</p>
<p>
<br>
</p>
<p>
A wholotta supplemental data:
</p>
<p>
<br>
MDRUN_MPI STD-I/O:<br>
==================<br>
<br>
step 0<br>
[hydrogen:15285] *** Process received signal ***<br>
[hydrogen:15285] Signal: Segmentation fault (11)<br>
[hydrogen:15285] Signal code: Address not mapped (1)<br>
[hydrogen:15285] Failing at address: 0xfffffffe16c50a90<br>
[hydrogen:15285] [ 0] /lib64/libpthread.so.0 [0x355c00de80]<br>
[hydrogen:15285] [ 1] mdrun_mpi(gmx_pme_do+0x28b2) [0x4b56f2]<br>
[hydrogen:15285] [ 2] mdrun_mpi(do_force_lowlevel+0x1023) [0x47f6f3]<br>
[hydrogen:15285] [ 3] mdrun_mpi(do_force+0xe6e) [0x4c99ce]<br>
[hydrogen:15285] [ 4] mdrun_mpi(do_md+0x48f0) [0x42c4a0]<br>
[hydrogen:15285] [ 5] mdrun_mpi(mdrunner+0x831) [0x42d771]<br>
[hydrogen:15285] [ 6] mdrun_mpi(main+0x3c0) [0x42e6a0]<br>
[hydrogen:15285] [ 7] /lib64/libc.so.6(__libc_start_main+0xf4) [0x355b41d8b4]<br>
[hydrogen:15285] [ 8] mdrun_mpi [0x4131a9]<br>
[hydrogen:15285] *** End of error message ***<br>
./test-2-6-09.sh: line 16: 15285 Segmentation fault mdrun_mpi -c md -v<br>
<br>
<br>
----------------------------------------------------------------------------------------------------------------<br>
<br>
MD.MDP<br>
======<br>
<br>
integrator = sd ;stochastic dynamics (velocity Langevin) using a leap-frog algorithm<br>
dt = 0.0001<br>
nsteps = 10000 ; [steps] ==> total (nsteps*dt) ps.<br>
nstxout = 1<br>
nstvout = 1<br>
nstfout = 1<br>
; nstxtcout = 1<br>
nstenergy = 1 ; write energies to energy file every 1000 steps (default 100)<br>
nstlog = 1<br>
energygrps = SL SR<br>
ns_type = simple<br>
periodic_molecules = no<br>
coulombtype = PME<br>
tc-grps = SL SR<br>
tau_t = 0 1 ; mass/gamma<br>
ref_t = 0 0 ; refference (bath) temperature<br>
Pcoupl = no<br>
gen_vel = no<br>
gen_seed = -1 ; random seed based on computer clock<br>
constraints = none<br>
<br>
--------------------------------------------------------------------------------------------<br>
<br>
1S2.itp<br>
=======<br>
<br>
[ atomtypes ]<br>
;atomtype m (u) q (e) part.type V(cr) W(cr)<br>
SX 32.0600 0.000 A 1E-03 1E-05<br>
<br>
[ moleculetype ]<br>
; Name nrexcl<br>
1S2 2<br>
<br>
[ atoms ]<br>
; nr type resnr resid atom cgnr charge mass<br>
1 SX 1 1S2 SL 1 0.000 32.0600<br>
2 SX 1 1S2 SR 2 0.000 32.0600<br>
<br>
[ bonds ]<br>
; ai aj fu c0, c1, ...<br>
1 2 2 0.2040 5.3E+6 0.2040 5.3E+6 ; SL SR<br>
<br>
--------------------------------------------------------------------------------------------<br>
<br>
TRAJ.TRR<br>
========<br>
<br>
traj.trr frame 0:<br>
natoms= 2 step= 0 time=0.0000000e+00 lambda= 0<br>
box (3x3):<br>
box[ 0]={ 6.37511e+00, 0.00000e+00, 0.00000e+00}<br>
box[ 1]={ 0.00000e+00, 6.37511e+00, 0.00000e+00}<br>
box[ 2]={ 0.00000e+00, 0.00000e+00, 6.37511e+00}<br>
x (2x3):<br>
x[ 0]={ 3.19756e+00, 3.20532e+00, 3.18725e+00}<br>
x[ 1]={ 3.03044e+00, 3.21568e+00, 3.08875e+00}<br>
v (2x3):<br>
v[ 0]={ 2.22763e+00, -2.56083e-01, 1.38905e+00}<br>
v[ 1]={-2.22763e+00, 2.56083e-01, -1.38905e+00}<br>
f (2x3):<br>
f[ 0]={ 3.43615e+03, -2.13216e+02, 2.02509e+03}<br>
f[ 1]={-3.43615e+03, 2.13216e+02, -2.02509e+03}<br>
<br>
<br>
--------------------------------------------------------------------------------------------<br>
<br>
MD.LOG<br>
======<br>
<br>
<br>
<br>
Input Parameters:<br>
integrator = sd<br>
nsteps = 10000<br>
init_step = 0<br>
ns_type = Simple<br>
nstlist = 10<br>
ndelta = 2<br>
nstcomm = 1<br>
comm_mode = Linear<br>
nstlog = 1<br>
nstxout = 1<br>
nstvout = 1<br>
nstfout = 1<br>
nstenergy = 1<br>
nstxtcout = 0<br>
init_t = 0<br>
delta_t = 0.0001<br>
xtcprec = 1000<br>
nkx = 54<br>
nky = 54<br>
nkz = 54<br>
pme_order = 4<br>
ewald_rtol = 1e-05<br>
ewald_geometry = 0<br>
epsilon_surface = 0<br>
optimize_fft = FALSE<br>
ePBC = xyz<br>
bPeriodicMols = FALSE<br>
bContinuation = FALSE<br>
bShakeSOR = FALSE<br>
etc = No<br>
epc = No<br>
epctype = Isotropic<br>
tau_p = 1<br>
ref_p (3x3):<br>
ref_p[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}<br>
ref_p[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}<br>
ref_p[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}<br>
compress (3x3):<br>
compress[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}<br>
compress[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}<br>
compress[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}<br>
refcoord_scaling = No<br>
posres_com (3):<br>
posres_com[0]= 0.00000e+00<br>
posres_com[1]= 0.00000e+00<br>
posres_com[2]= 0.00000e+00<br>
posres_comB (3):<br>
posres_comB[0]= 0.00000e+00<br>
posres_comB[1]= 0.00000e+00<br>
posres_comB[2]= 0.00000e+00<br>
andersen_seed = 815131<br>
rlist = 1<br>
rtpi = 0.05<br>
coulombtype = PME<br>
rcoulomb_switch = 0<br>
rcoulomb = 1<br>
vdwtype = Cut-off<br>
rvdw_switch = 0<br>
rvdw = 1<br>
epsilon_r = 1<br>
epsilon_rf = 1<br>
tabext = 1<br>
implicit_solvent = No<br>
gb_algorithm = Still<br>
gb_epsilon_solvent = 80<br>
nstgbradii = 1<br>
rgbradii = 2<br>
gb_saltconc = 0<br>
gb_obc_alpha = 1<br>
gb_obc_beta = 0.8<br>
gb_obc_gamma = 4.85<br>
sa_surface_tension = 2.092<br>
DispCorr = No<br>
free_energy = no<br>
init_lambda = 0<br>
sc_alpha = 0<br>
sc_power = 0<br>
sc_sigma = 0.3<br>
delta_lambda = 0<br>
nwall = 0<br>
wall_type = 9-3<br>
wall_atomtype[0] = -1<br>
wall_atomtype[1] = -1<br>
wall_density[0] = 0<br>
wall_density[1] = 0<br>
wall_ewald_zfac = 3<br>
pull = no<br>
disre = No<br>
disre_weighting = Conservative<br>
disre_mixed = FALSE<br>
dr_fc = 1000<br>
dr_tau = 0<br>
nstdisreout = 100<br>
orires_fc = 0<br>
orires_tau = 0<br>
nstorireout = 100<br>
dihre-fc = 1000<br>
em_stepsize = 0.01<br>
em_tol = 10<br>
niter = 20<br>
fc_stepsize = 0<br>
nstcgsteep = 1000<br>
nbfgscorr = 10<br>
ConstAlg = Lincs<br>
shake_tol = 0.0001<br>
lincs_order = 4<br>
lincs_warnangle = 30<br>
lincs_iter = 1<br>
bd_fric = 0<br>
ld_seed = 1993<br>
cos_accel = 0<br>
deform (3x3):<br>
deform[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}<br>
deform[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}<br>
deform[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}<br>
userint1 = 0<br>
userint2 = 0<br>
userint3 = 0<br>
userint4 = 0<br>
userreal1 = 0<br>
userreal2 = 0<br>
userreal3 = 0<br>
userreal4 = 0<br>
grpopts:<br>
nrdf: 1.5 1.5<br>
ref_t: 0 0<br>
tau_t: 0 1<br>
anneal: No No<br>
ann_npoints: 0 0<br>
acc: 0 0 0<br>
nfreeze: N N N<br>
energygrp_flags[ 0]: 0 0<br>
energygrp_flags[ 1]: 0 0<br>
efield-x:<br>
n = 0<br>
efield-xt:<br>
n = 0<br>
efield-y:<br>
n = 0<br>
efield-yt:<br>
n = 0<br>
efield-z:<br>
n = 0<br>
efield-zt:<br>
n = 0<br>
bQMMM = FALSE<br>
QMconstraints = 0<br>
QMMMscheme = 0<br>
scalefactor = 1<br>
qm_opts:<br>
ngQM = 0<br>
Table routines are used for coulomb: TRUE<br>
Table routines are used for vdw: FALSE<br>
Will do PME sum in reciprocal space.<br>
<br>
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++<br>
U. Essman, L. Perela, M. L. Berkowitz, T. Darden, H. Lee and L. G. Pedersen<br>
A smooth particle mesh Ewald method<br>
J. Chem. Phys. 103 (1995) pp. 8577-8592<br>
-------- -------- --- Thank You --- -------- --------<br>
<br>
Using a Gaussian width (1/beta) of 0.320163 nm for Ewald<br>
Cut-off's: NS: 1 Coulomb: 1 LJ: 1<br>
System total charge: 0.000<br>
Generated table with 4000 data points for Ewald.<br>
Tabscale = 2000 points/nm<br>
Generated table with 4000 data points for LJ6.<br>
Tabscale = 2000 points/nm<br>
Generated table with 4000 data points for LJ12.<br>
Tabscale = 2000 points/nm<br>
Configuring nonbonded kernels...<br>
Testing x86_64 SSE2 support... present.<br>
<br>
<br>
Removing pbc first time<br>
Center of mass motion removal mode is Linear<br>
We have the following groups for center of mass motion removal:<br>
0: rest<br>
There are: 2 Atoms<br>
Max number of connections per atom is 1<br>
Total number of connections is 2<br>
Max number of graph edges per atom is 1<br>
Total number of graph edges is 2<br>
Initial temperature: 17884.7 K<br>
<br>
Started mdrun on node 0 Tue Jun 2 13:38:03 2009<br>
<br>
Step Time Lambda<br>
0 0.00000 0.00000<br>
<br>
Energies (kJ/mol)<br>
G96Bond LJ (SR) Coulomb (SR) Coul. recip. Potential<br>
1.99416e+01 0.00000e+00 0.00000e+00 0.00000e+00 1.99416e+01<br>
Kinetic En. Total Energy Temperature Pressure (bar)<br>
nan nan nan nan<br>
<br>
Step Time Lambda<br>
1 0.00010 0.00000<br>
<br>
</p>
<p>
<br>
</p>
<p>
--<br>
Inon Sharony<br>
ינון שרוני<br>
+972(3)6407634<br>
<a href="http://atto.TAU.ac.IL/~inonshar" target="_blank">atto.TAU.ac.IL/~inonshar</a><br>
Please consider your environmental responsibility before printing this e-mail.
</p>
</div>
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