Hello Justin,<br><br>Thanks for you reply. My late response is because I have been trying to resolve the problem. <br><br>
<div class="gmail_quote"><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div class="im"><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Dear experts,<br>
<br>
I am trying to build up a polymer in hexane system by increasing the density. After PR step, my NVT and NPT trailes failed. Initially I used to get LINCS and 1-4 warnings (even for NVT) which were not because of flawed topology file. It turned out that simulations crashed just because of using -np > 4. But still even with this -np, NPT did not work which made me to swtich to berendsen from parrinelo rahman scheme. As I approched the desired density again simulation crashed, so I used<br>
<br>
trjconv -s .tpr -f .trr -o frame2300.gro -dump 2300<br>
<br>
to extract one of the frames before crash I did another NVT to equilibrate.<br>
mpirun -np 4 mdrun_mpi -deffnm PE60-110Hex-NPT3-frame2300_md -s -o -c -g -e -x -v -pd<br>
<br>
after around 1 ns I get the error below ( mdp file is also included). I described above since I encountered the situation where root cause of problem was not topology and just the computational issue ( I mean -np), I am just curious if the same thing applies here. Please help me with this. Thank you in advance.<br>
<br>
</blockquote>
<br></div>
What MPI library (and version) are you using? Do your runs work in serial?<div class="im"><br></div></blockquote><div>I am using openmpi.1.4.3. Once I try mdrun in serial I get many LINCS and 1-4 warnings ending with segmentation fault at the very beginning. <br>
<br>Wrote pdb files with previous and current coordinates<br>Wrote pdb files with previous and current coordinates<br>Warning: 1-4 interaction between 1433 and 1441 at distance 2.472 which is larger than the 1-4 table size 2.250 nm<br>
These are ignored for the rest of the simulation<br>This usually means your system is exploding,<br>if not, you should increase table-extension in your mdp file<br>or with user tables increase the table size<br><br>Step 11, time 0.022 (ps) LINCS WARNING<br>
relative constraint deviation after LINCS:<br>rms 0.004346, max 0.036836 (between atoms 116 and 119)<br><br>parallel run does not work for -np >4<br><br></div><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<div class="im">
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
more details: There is only one polyethylene chain ( 60 units) in 110 hexane. The chain is not convoluted and has a little extended shape, which make it not easy fit in the box.<br>
<br>
</blockquote>
<br></div>
What do you mean it doesn't fit in the box? If you've got a system that you're trying to force into some shape or size, your PE chain is probably just crashing into itself across periodic boundaries. Watch the trajectory to see what's going on prior to the crash.<br>
</blockquote><div><br><br>I am not forcing it in to the box. I am just increasing the density but since it becomes to extended it crashes into itself as you predicted. I have no control on this..Then I had to take another frame before crash and try a new conformation hoping that a long simulation with this starting structure does not crash.<br>
<br>Also I tried FE, but I am getting no output file dhdl. even when I include -dhdl in the command line...<br><br>free_energy = yes<br>init_lambda = 0 <br>delta_lambda = 0<br>sc_alpha = 0.5<br>
sc-power = 1<br>sc_sigma = 0.3<br>foreign_lambda = 0.1<br>dhdl_derivatives = yes<br>couple-moltype = Polymer<br>couple-lambda0 = vdw-q ;vdw<br>couple-lambda1 = none ;vdw;none<br>
couple-intramol = yes<br>nstdhdl = 10<br>separate_dhdl_file = yes<br>dh_hist_size = 0<br>dh_hist_spacing = 0.1<br><br>Please give me some advice..<br>Thanks <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>
-Justin<div><div></div><div class="h5"><br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Moeed<br>
===========================================<br>
<br>
step 449800, will finish Tue Mar 15 11:23:55 2011<br>
step 449900, will finish Tue Mar 15 11:23:55 2011<br>
[node5:09563] *** Process received signal ***<br>
[node5:09563] Signal: Segmentation fault (11)<br>
[node5:09563] Signal code: Address not mapped (1)<br>
[node5:09563] Failing at address: 0xffffffff80849dc0<br>
[node5:09563] [ 0] /lib64/libpthread.so.0 [0x3a2660eb10]<br>
[node5:09563] [ 1] mdrun_mpi [0x4f0155]<br>
[node5:09563] [ 2] mdrun_mpi(gmx_pme_do+0x216d) [0x4f9c1d]<br>
[node5:09563] [ 3] mdrun_mpi(do_force_lowlevel+0x21c8) [0x49c658]<br>
[node5:09563] [ 4] mdrun_mpi(do_force+0xc59) [0x50db19]<br>
[node5:09563] [ 5] mdrun_mpi(do_md+0x5623) [0x43e353]<br>
[node5:09563] [ 6] mdrun_mpi(mdrunner+0xa07) [0x435e07]<br>
[node5:09563] [ 7] mdrun_mpi(main+0x1269) [0x443319]<br>
[node5:09563] [ 8] /lib64/libc.so.6(__libc_start_main+0xf4) [0x3a25e1d994]<br>
[node5:09563] [ 9] mdrun_mpi [0x420449]<br>
[node5:09563] *** End of error message ***<br>
--------------------------------------------------------------------------<br>
mpirun noticed that process rank 0 with PID 9563 on node node5.reyclus.loc exited on signal 11 (Segmentation fault).<br>
-----------------------------------------------------------------------<br>
<br>
<br>
<br>
pbc = xyz ;energygrps = PE HEX<br>
; Run control integrator = md dt = 0.002 nsteps = 1000000 ;5000 nstcomm = 100 <br>
; Output control<br>
nstenergy = 100 nstxout = 100 nstvout = 0<br>
nstfout = 0<br>
nstlog = 1000 nstxtcout = 1000 <br>
; Neighbor searching<br>
nstlist = 10 ns_type = grid <br>
; Electrostatics/VdW<br>
coulombtype = PME vdw-type = Shift rcoulomb-switch = 0 rvdw-switch = 0.9 ;0 <br>
; Cut-offs<br>
rlist = 1.25 rcoulomb = 1.25 ;1.1 rvdw = 1.0 <br>
; PME parameters<br>
fourierspacing = 0.12 fourier_nx = 0<br>
fourier_ny = 0<br>
fourier_nz = 0<br>
pme_order = 4 ewald_rtol = 1e-5<br>
optimize_fft = yes<br>
<br>
; Temperature coupling Tcoupl = v-rescale tc-grps = System ;HEX tau_t = 0.1 ;0.1 ref_t = 300 ;300 ; Pressure coupling<br>
Pcoupl = no;berendsen Pcoupltype = isotropic tau_p = 0.5 ;0.5 compressibility = 4.5e-5 4.5e-5 ref_p = 30 30 <br>
; Velocity generation gen_vel = yes gen_temp = 300.0 gen_seed = 173529 <br>
; Bonds<br>
constraints = all-bonds constraint-algorithm = lincs<br>
<br>
</blockquote>
<br></div></div>
-- <br>
========================================<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> | (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>
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