Hello Justin,<br><br>I just scanned through the manual and also looked into the list to learn about the significance of reciprocal part to realize your statement. I did not find much about the fact that how I can judge if fourierspacing is the cause of the crash (I mean relevance between fourierspacing and coulb recip). I suspect the cause of crashes is because of electrostatics settings. BEfore that I had only vdw no run crashed. Since I used to get LINCS warning I removed bond constraints but still system is showing instabilities. I am confident that topology is fine and just wondering how else one can inspect root cause for unphysical forces.<br>
<br><br>fourierspacing =0.12 : Coul. recip. 636.217 8.69433 8.62908 0.0167398 3.68278<br><br>fourierspacing =0.3 : Coul. recip. 642.921 6.06063 6.02832 -0.00984063 -2.16496<br>
<br><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;">
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Everything has a cause; nothing is accidental. No stable run should ever show LINCS warnings like this, so yes, there is something to fix.<br>
<br>
You also have not proven that your fourierspacing is not the cause. The proper term to analyze is Coul-recip, which corresponds to reciprocal space Coulombic term. I don't see that listed below.<br>
<br>
-Justin<div><div></div><div class="h5"><br>
<br>
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Thanks,<br>
Best,<br>
Moeed<br>
<br>
========================================<br>
step 164300, remaining runtime: 241 s step 164400, remaining runtime: 240 s step 164500, remaining runtime: 240 s step 164600, remaining runtime: 239 s Warning: 1-4 interaction between 260 and 267 at distance 73679654.990 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>
results till t=320 ps (before first run crash)<br>
fourierspacing = 0.12<br>
<br>
LJ-14 757.246 26.6239 26.5661 -0.0189929 -6.07777<br>
<br>
Coulomb-14 -186.509 15.9866 15.9529 -0.0112174 -3.5896<br>
<br>
LJ (SR) -2691.84 117.026 107.231 -0.507373 -162.361<br>
<br>
Coulomb (SR) 725.662 17.6483 17.5876 0.0158275 5.06483<br>
<br>
<br>
fourierspacing = 0.3<br>
<br>
<br>
LJ-14 757.129 26.4936 26.4578 -0.0149128 -4.77214<br>
<br>
Coulomb-14 -199.523 14.949 14.158 -0.0519427 -16.6218<br>
<br>
LJ (SR) -2670.5 111.201 109.688 0.19784 63.3092<br>
<br>
Coulomb (SR) 739.794 16.1807 15.4473 0.0521352 16.6834<br>
<br>
====================================================<br>
pbc = xyz <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 = 0.3 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 = 400 ;300 <br>
; Pressure coupling<br>
Pcoupl = Parrinello-Rahman Pcoupltype = isotropic tau_p = 1 1 ;0.5 compressibility = 4.5e-5 4.5e-5 ref_p = 70 70 <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>
========================================<br><font color="#888888">
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</font></blockquote></div><br><br clear="all"><br>-- <br>Moeed Shahamat<br>Graduate Student (Materials Modeling Research Group)<br>McGill University- Department of Chemical Engineering<br>Montreal, Quebec H3A 2B2, Canada<br>
Web:<a href="http://mmrg.chemeng.mcgill.ca/pages/current-group-members/moeed-shahamat.php">http://mmrg.chemeng.mcgill.ca/pages/current-group-members/moeed-shahamat.php</a><br>Web:<a href="http://mmrg.chemeng.mcgill.ca/">http://mmrg.chemeng.mcgill.ca/</a><br>