<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">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 class="im">
<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 class="im">
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>><u></u>>__><div class="im">
<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>><u></u>>__><div class="im">
<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 class="h5">
<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/___<u></u>_issues/777</a><br>
<<a href="http://redmine.gromacs.org/__issues/777" target="_blank">http://redmine.gromacs.org/__<u></u>issues/777</a>><div class="im"><br>
<<a href="http://redmine.gromacs.org/__issues/777" target="_blank">http://redmine.gromacs.org/__<u></u>issues/777</a><br>
<<a href="http://redmine.gromacs.org/issues/777" target="_blank">http://redmine.gromacs.org/<u></u>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 class="HOEnZb"><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><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">
<span class="HOEnZb"><font color="#888888">
<br>
-Justin</font></span><div class="HOEnZb"><div class="h5"><br>
<br>
-- <br>
==============================<u></u>==========<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | <a href="tel:%28540%29%20231-9080" value="+15402319080" target="_blank">(540) 231-9080</a><br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.<u></u>vt.edu/Pages/Personal/justin</a><br>
<br>
==============================<u></u>==========<br>
-- <br>
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