Steven Neumann wrote:
On Thu, Mar 1, 2012 at 5:43 PM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
Steven Neumann wrote:
On Thu, Mar 1, 2012 at 3:58 PM, Steven Neumann
<s.neuman...@gmail.com <mailto:s.neuman...@gmail.com>
<mailto:s.neuman...@gmail.com <mailto:s.neuman...@gmail.com>>__>
wrote:
On Thu, Mar 1, 2012 at 3:32 PM, Steven Neumann
<s.neuman...@gmail.com <mailto:s.neuman...@gmail.com>
<mailto:s.neuman...@gmail.com <mailto:s.neuman...@gmail.com>>__>
wrote:
On Thu, Mar 1, 2012 at 2:55 PM, Justin A. Lemkul
<jalem...@vt.edu <mailto:jalem...@vt.edu>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>> wrote:
Steven Neumann wrote:
Dear Gmx Users,
I am trying to run nvt simulation (equilibration) of
the protein in implicit solvent. My mdp:
integrator = md ; leap-frog
integrator
nsteps = 1000000 ; 0.0005 * 1000000 = 0.5 ns
dt = 0.0005 ; 0.5 fs
; Output control
nstxout = 10000
nstxtcout = 10000 ; xtc compressed trajectory output
every 2 ps
nstenergy = 10000 ; save energies every 2 ps
nstlog = 10000 ; update log file every 2 ps
; Bond parameters
continuation = no
constraints = none
; Neighborsearching
ns_type = simple ; search neighboring grid cells
nstlist = 0 ; 10 fs
rlist = 0 ; short-range neighborlist cutoff (in nm)
; Infinite box with no cutoffs
pbc = no
rcoulomb = 0 ; short-range electrostatic cutoff
(in nm)
coulombtype = cut-off
vdwtype = cut-off
rvdw = 0 ; short-range van der Waals cutoff (in nm)
epsilon_rf = 0
comm_mode = angular ; remove angular and com motions
; implicit solvent
implicit_solvent = GBSA
gb_algorithm = OBC
gb_epsilon_solvent = 80.0
sa_surface_tension = 2.25936
rgbradii = 0
sa_algorithm = Ace-approximation
nstgbradii = 1
; Temperature coupling is on
Tcoupl = v-rescale
tau_t = 0.1
tc_grps = system
ref_t = 298
; Velocity generation
gen_vel = yes ; Velocity generation is on
gen_temp = 298.0
gen_seed = -1
Then after grompp I am trying to run the
simulation on
the cluster:
mdrun -pd -deffnm nvt500ps
My log file:
Back Off! I just backed up nvt500ps.log to
./#nvt500ps.log.1#
Reading file nvt500ps.tpr, VERSION 4.5.4 (single
precision)
Starting 8 threads
Back Off! I just backed up nvt500ps.trr to
./#nvt500ps.trr.1#
Back Off! I just backed up nvt500ps.xtc to
./#nvt500ps.xtc.1#
Back Off! I just backed up nvt500ps.edr to
./#nvt500ps.edr.1#
starting mdrun 'Protein'
1000000 steps, 500.0 ps.
Segmentation fault
Do you have any clue what is
happening?
Try running in serial or with a maximum of 2 threads.
Your
problem could be related to
http://redmine.gromacs.org/____issues/777
<http://redmine.gromacs.org/__issues/777>
<http://redmine.gromacs.org/__issues/777
<http://redmine.gromacs.org/issues/777>>. You will need to
upgrade to 4.5.5 (serial should work on 4.5.4).
-Justin
Thank you. What do you mean by running in
serial? Well... with 2
threads it does not make sense to use implicit solvent. Will
4.5.5 resolve this problem?
Indeed, it works in serial. Will version 4.5.5 resolve
it run it on
e.g. 12 nodes?
Sorry, the same problem :
I think, as stated in the redmine issue cited before, the limit is 2
threads/processors.
-Justin
I tried on one thread and on two threads and the error is still the
same. Without particle decomposition the problem remains. Any suggestions?
Then the problem lies outside of the algorithms. Your system has become
instantly unstable, thus suggesting that you have not sufficiently minimized or
equilibrated the structure.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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