Hi Justin,<br>
<br>
Sorry I didn't include all of my md.mdp file, as it is quite long :).
I have included as a reference below. I've taken a look at the log file, but I'm not really sure what I should be looking for so to identify what is causing my system to blow up? Should I start with the energies (see below)?<br>
<br>Finally, I've read through the "Blowing up" link you sent me. Taking it into consideration, do you suggest that I lower my timestep in my em.mdp file? It's already at dt = 0.02?<br><br>Thanks!<br>
Lily<br><br><br>~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~<br><b>log file<br><br></b>++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++<br>H. J. C. Berendsen, J. P. M. Postma, A. DiNola and J. R. Haak<br>
Molecular dynamics with coupling to an external bath<br>J. Chem. Phys. 81 (1984) pp. 3684-3690<br>-------- -------- --- Thank You --- -------- --------<br> <br> Rel. Constraint Deviation: Max between atoms RMS<br>
Before LINCS 0.030283 453 454 0.008216<br> After LINCS 0.000040 1278 1276 0.000011<br> <br> Energies (kJ/mol) <br> Bond G96Angle LJ (SR) Coulomb (SR) Potential<br>
4.22829e+03 7.72020e+03 -6.51083e+06 5.87935e+01 -6.49883e+06<br> Kinetic En. Total Energy Temperature Pressure (bar)<br> 9.04109e+05 -5.59472e+06 3.10086e+02 -2.18809e+03<br>~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~<br>
<br><br><br>~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~<br><b>md.mdp file</b><br>
<br>
<br>
integrator = md<br>
; start time and timestep in ps<br>
tinit = 0<br>
dt = 0.020<br>
;nsteps = 10000 ; initial step<br>
nsteps = 10000000 ; 200 ns @ dt=0.02<br>
<br>
; number of steps for center of mass motion removal =<br>
nstcomm = 1<br>
comm-grps =<br>
<br>
; OUTPUT CONTROL OPTIONS =<br>
; Output frequency for coords (x), velocities (v) and forces (f) =<br>
nstxout = 5000<br>
nstvout = 5000<br>
nstfout = 0<br>
; Output frequency for energies to log file and energy file =<br>
nstlog = 1000<br>
nstenergy = 1000<br>
; Output frequency and precision for xtc file =<br>
nstxtcout = 10000 ; frame every 150 ps<br>
xtc_precision = 1000<br>
; This selects the subset of atoms for the xtc file. You can = <br>
; select multiple groups. By default all atoms will be written. =<br>
xtc-grps = <br>
; Selection of energy groups = <br>
energygrps = PROTEIN W ION<br>
<br>
; NEIGHBORSEARCHING PARAMETERS =<br>
; MARTINI - no need for more frequent updates <br>
; or larger neighborlist cut-off due<br>
; to the use of shifted potential energy functions.<br>
<br>
; nblist update frequency =<br>
nstlist = 10<br>
; ns algorithm (simple or grid) = <br>
ns_type = grid <br>
; Periodic boundary conditions: xyz or none = <br>
pbc = xyz<br>
; nblist cut-off =<br>
rlist = 1.2<br>
<br>
; OPTIONS FOR ELECTROSTATICS AND VDW =<br>
; MARTINI - vdw and electrostatic interactions are used<br>
; in their shifted forms. Changing to other types of<br>
; electrostatics will affect the general performance of<br>
; the model.<br>
<br>
; Method for doing electrostatics =<br>
coulombtype = Shift <br>
rcoulomb_switch = 0.0<br>
rcoulomb = 1.2<br>
; Dielectric constant (DC) for cut-off or DC of reaction field =<br>
epsilon_r = 15<br>
; Method for doing Van der Waals =<br>
vdw_type = Shift <br>
; cut-off lengths = <br>
rvdw_switch = 0.9<br>
rvdw = 1.2 <br>
; Apply long range dispersion corrections for Energy and Pressure =<br>
DispCorr = No<br>
<br>
; OPTIONS FOR WEAK COUPLING ALGORITHMS = <br>
; MARTINI - normal temperature and pressure coupling schemes<br>
; can be used. It is recommended to couple individual groups<br>
; in your system seperately.<br>
<br>
; Temperature coupling =<br>
tcoupl = Berendsen<br>
; Groups to couple separately =<br>
tc-grps = PROTEIN SOLVENT<br>
; Time constant (ps) and reference temperature (K) =<br>
tau_t = 1.0 1.0<br>
ref_t = 310 310<br>
; Pressure coupling =<br>
Pcoupl = berendsen<br>
Pcoupltype = isotropic<br>
; Time constant (ps), compressibility (1/bar) and reference P (bar) =<br>
tau_p = 5.0<br>
compressibility = 4.5e-5<br>
ref_p = 1.0<br>
<br>
; GENERATE VELOCITIES FOR STARTUP RUN =<br>
gen_vel = yes<br>
gen_temp = 310<br>
gen_seed = 1<br>
<br>
; OPTIONS FOR BONDS =<br>
; MARTINI - for ring systems constraints are defined<br>
; which are best handled using Lincs.<br>
constraints = none<br>
; Type of constraint algorithm =<br>
constraint_algorithm = Lincs<br>
; Do not constrain the start configuration =<br>
unconstrained_start = no<br>
; Highest order in the expansion of the constraint coupling matrix =<br>
lincs_order = 4<br>
; Lincs will write a warning to the stderr if in one step a bond =<br>
; rotates over more degrees than =<br>
lincs_warnangle = 30<br><br>
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~<br><br><div class="gmail_quote">2009/11/13 Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span><br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div><div></div><div class="h5"><br>
<br>
<a href="mailto:rainy908@yahoo.com" target="_blank">rainy908@yahoo.com</a> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi all,<br>
<br>
I've encountered a problem while trying to run Gromacs on my coarse-grained molecule. I've already performed the initial energy minimization. I tried to run the inital MD simulation, but the job was cut short due to a segmentation fault, as mentioned in the output file:<br>
<br>
^Mstep 0^Mstep 100, will finish Wed Dec 16 16:55:17 2009^Mstep 200, will finish Wed Dec 16 07:04:11 2009^Mstep 300, will finish Wed Dec 16 12:59:33 2009^Mstep 400, will finish Wed Dec 16 09:02:03 2009^Mstep 500, will finish Wed Dec 16 12:12:01 2009^Mstep 600, will finish Wed Dec 16 14:18:47 2009^Mstep 700, will finish Wed Dec 16 15:49:22 2009^Mstep 800, will finish Wed Dec 16 13:29:16 2009^Mstep 900, will finish Wed Dec 16 14:45:15 2009^Mstep 1000, will finish Wed Dec 16 15:46:03 2009<br>
<br>
/opt/gridengine/default/spool/<br>
compute-0-7/job_scripts/182710: line 28: 18851 Segmentation fault (core dumped) $MDRUN -v -nice 0 -np $NSLOTS -s npg3_4.tpr -o npg3_4.trr -c confout.gro -g npg3_4.log -x npg3_4.xtc -e npg3_4.edr<br>
/opt/gridengine/default/spool/compute-0-7/job_scripts/182710: line 31: -s: command not found<br>
<br>
Does anyone know what could be causing the problem? Should it be of interest, my em.mdp is included at the bottom.<br>
<br>
Thanks for your help!<br>
<br>
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~<br>
em.mdp<br>
; VARIOUS PREPROCESSING OPTIONS =<br>
title =<br>
cpp = /lib/cpp<br>
include =<br>
define =<br>
<br>
; RUN CONTROL PARAMETERS =<br>
integrator = steep<br>
; start time and timestep in ps =<br>
tinit = 0<br>
dt = 0.02<br>
nsteps = 1000<br>
<br>
; ENERGY MINIMIZATION OPTIONS =<br>
;emtol = 0.00001<br>
;emstep = 0.1<br>
;nstcgsteep = 1000<br>
<br>
emtol = 10<br>
emstep = 0.01<br>
nstcgsteep = 1000<br>
<br>
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~<br>
<br>
md.mdp<br>
<br>
; RUN CONTROL PARAMETERS =<br>
; MARTINI - Most simulations are stable with dt=40 fs,<br>
; some (especially rings) require 20-30 fs.<br>
; The range of time steps used for parametrization<br>
; is 20-40 fs, using smaller time steps is therefore not recommended.<br>
<br>
integrator = md<br>
; start time and timestep in ps<br>
tinit = 0<br>
dt = 0.020<br>
;nsteps = 10000 ; initial step<br>
nsteps = 10000000 ; 200 ns @ dt=0.02<br>
<br>
; number of steps for center of mass motion removal =<br>
nstcomm = 1<br>
comm-grps =<br>
<br>
</blockquote>
<br></div></div>
Is this the entirety of your md.mdp file? If so, all other options will be set to default, and these may or may not (read: likely will not) be appropriate for your system. A number of factors can lead to a segmentation fault, but in generic terms, something became unstable. Check the output - look at the trajectory to see where things start to fall apart. Helpful messages are usually printed in the log file as well. Beyond that, please consult the following:<br>
<br>
<a href="http://www.gromacs.org/Documentation/Terminology/Blowing_Up" target="_blank">http://www.gromacs.org/Documentation/Terminology/Blowing_Up</a><br>
<br>
-Justin<br>
<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<br><font color="#888888">
-- <br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br>
</font></blockquote></div><br><br>