<br><br><div class="gmail_quote">On Thu, Mar 1, 2012 at 10:26 PM, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000"><div><div class="h5">
On 2/03/2012 9:22 AM, Steven Neumann wrote:
<blockquote type="cite"><br>
<br>
<div class="gmail_quote">On Thu, Mar 1, 2012 at 10:07 PM, Justin
A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
<br>
Steven Neumann wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div>
<br>
<br>
On Thu, Mar 1, 2012 at 5:43 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>> wrote:<br>
<br>
<br>
<br>
Steven Neumann wrote:<br>
<br>
<br>
<br>
</div>
<div> On Thu, Mar 1, 2012 at 3:58 PM,
Steven Neumann<br>
<<a href="mailto:s.neumann08@gmail.com" target="_blank">s.neumann08@gmail.com</a>
<mailto:<a href="mailto:s.neumann08@gmail.com" target="_blank">s.neumann08@gmail.com</a>><br>
</div>
<mailto:<a href="mailto:s.neumann08@gmail.com" target="_blank">s.neumann08@gmail.com</a>
<mailto:<a href="mailto:s.neumann08@gmail.com" target="_blank">s.neumann08@gmail.com</a>>>__>
<div>
<br>
wrote:<br>
<br>
<br>
<br>
On Thu, Mar 1, 2012 at 3:32 PM, Steven Neumann<br>
<<a href="mailto:s.neumann08@gmail.com" target="_blank">s.neumann08@gmail.com</a>
<mailto:<a href="mailto:s.neumann08@gmail.com" target="_blank">s.neumann08@gmail.com</a>><br>
</div>
<mailto:<a href="mailto:s.neumann08@gmail.com" target="_blank">s.neumann08@gmail.com</a>
<mailto:<a href="mailto:s.neumann08@gmail.com" target="_blank">s.neumann08@gmail.com</a>>>__>
<div>
<br>
wrote:<br>
<br>
<br>
<br>
On Thu, Mar 1, 2012 at 2:55 PM, Justin A.
Lemkul<br>
<<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>
<mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>><br>
</div>
<div>
<div> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>>> wrote:<br>
<br>
<br>
<br>
Steven Neumann wrote:<br>
<br>
Dear Gmx Users,<br>
I am trying to run nvt simulation
(equilibration) of<br>
the protein in implicit solvent.
My mdp:<br>
integrator = md ;
leap-frog<br>
integrator<br>
<br>
nsteps = 1000000 ; 0.0005 *
1000000 = 0.5 ns<br>
<br>
dt = 0.0005 ; 0.5 fs<br>
<br>
; Output control<br>
<br>
nstxout = 10000<br>
<br>
nstxtcout = 10000 ; xtc compressed
trajectory output<br>
every 2 ps<br>
<br>
nstenergy = 10000 ; save energies
every 2 ps<br>
<br>
nstlog = 10000 ; update log file
every 2 ps<br>
<br>
; Bond parameters<br>
<br>
continuation = no<br>
<br>
constraints = none<br>
<br>
; Neighborsearching<br>
<br>
ns_type = simple ; search
neighboring grid cells<br>
<br>
nstlist = 0 ; 10 fs<br>
<br>
rlist = 0 ; short-range
neighborlist cutoff (in nm)<br>
<br>
; Infinite box with no cutoffs<br>
<br>
pbc = no<br>
<br>
rcoulomb = 0 ; short-range
electrostatic cutoff<br>
(in nm)<br>
<br>
coulombtype = cut-off<br>
<br>
vdwtype = cut-off<br>
<br>
rvdw = 0 ; short-range van der
Waals cutoff (in nm)<br>
<br>
epsilon_rf = 0<br>
<br>
comm_mode = angular ; remove
angular and com motions<br>
<br>
; implicit solvent<br>
<br>
implicit_solvent = GBSA<br>
<br>
gb_algorithm = OBC<br>
<br>
gb_epsilon_solvent = 80.0<br>
<br>
sa_surface_tension = 2.25936<br>
<br>
rgbradii = 0<br>
<br>
sa_algorithm = Ace-approximation<br>
<br>
nstgbradii = 1<br>
<br>
; Temperature coupling is on<br>
<br>
Tcoupl = v-rescale<br>
<br>
tau_t = 0.1<br>
<br>
tc_grps = system<br>
<br>
ref_t = 298<br>
<br>
; Velocity generation<br>
<br>
gen_vel = yes ; Velocity
generation is on<br>
<br>
gen_temp = 298.0<br>
<br>
gen_seed = -1<br>
<br>
Then after grompp I am trying to
run the<br>
simulation on<br>
the cluster:<br>
<br>
mdrun -pd -deffnm nvt500ps<br>
<br>
My log file:<br>
<br>
Back Off! I just backed up
nvt500ps.log to<br>
./#nvt500ps.log.1#<br>
<br>
Reading file nvt500ps.tpr, VERSION
4.5.4 (single<br>
precision)<br>
<br>
Starting 8 threads<br>
<br>
Back Off! I just backed up
nvt500ps.trr to<br>
./#nvt500ps.trr.1#<br>
<br>
Back Off! I just backed up
nvt500ps.xtc to<br>
./#nvt500ps.xtc.1#<br>
<br>
Back Off! I just backed up
nvt500ps.edr to<br>
./#nvt500ps.edr.1#<br>
<br>
starting mdrun 'Protein'<br>
<br>
1000000 steps, 500.0 ps.<br>
<br>
Segmentation fault<br>
<br>
Do you have any
clue what is<br>
happening?<br>
<br>
<br>
Try running in serial or with a
maximum of 2 threads.<br>
Your<br>
problem could be related to<br>
</div>
</div>
<a href="http://redmine.gromacs.org/____issues/777" target="_blank">http://redmine.gromacs.org/____issues/777</a><br>
<<a href="http://redmine.gromacs.org/__issues/777" target="_blank">http://redmine.gromacs.org/__issues/777</a>>
<div><br>
<<a href="http://redmine.gromacs.org/__issues/777" target="_blank">http://redmine.gromacs.org/__issues/777</a><br>
<<a href="http://redmine.gromacs.org/issues/777" target="_blank">http://redmine.gromacs.org/issues/777</a>>>.
You will need to<br>
<br>
upgrade to 4.5.5 (serial should work on
4.5.4).<br>
<br>
-Justin<br>
<br>
Thank you. What do you mean by
running in<br>
serial? Well... with 2<br>
threads it does not make sense to use
implicit solvent. Will<br>
4.5.5 resolve this problem?<br>
Indeed, it works in serial.
Will version 4.5.5 resolve<br>
it run it on<br>
e.g. 12 nodes?<br>
Sorry, the same problem :<br>
<br>
<br>
I think, as stated in the redmine issue cited before,
the limit is 2<br>
threads/processors.<br>
<br>
-Justin<br>
<br>
<br>
<br>
I tried on one thread and on two threads and the error is
still the same. Without particle decomposition the problem
remains. Any suggestions?<br>
<br>
</div>
</blockquote>
<br>
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.<span><font color="#888888"><br>
</font></span></blockquote>
<div><br>
<br>
I run the same simulation with cutoff of 2.0 and it works
fine. Does it mean I cannot use vdw and coulombic cutoff set
to 0? It would be more realistic.<br>
</div>
</div>
</blockquote>
<br></div></div>
Thus you have an unstable initial system, and can get lucky under
some conditions. Follow the advice here to explore how you can
increase the chance of being lucky under your desired conditions: <a href="http://www.gromacs.org/Documentation/Terminology/Blowing_Up" target="_blank">http://www.gromacs.org/Documentation/Terminology/Blowing_Up</a>.
Or use the end point of the rc=2.0 simulation as input for one with
rc=0.<span class="HOEnZb"><font color="#888888"><br>
<br>
Mark<br>
</font></span></div>
<br></blockquote><div>Thank you Mark!<br><br>Steven <br></div><blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">--<br>
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