Dear experts,<br><br>I have been trying to do NVT on a system (a single polyethylene chain in 110 hexane) in the past few days but still no success. For some reason simulations are taking much longer than before. A run that used to complete in a few hours is taking several weeks. I am wondering if there is something wrong with our cluster or..my runs crash (LINCS) at early stages of simulation.<br>
<br>step 100, will finish Wed Mar 16 00:08:53 2011<br>step 200, will finish Wed Mar 16 00:05:57 2011<br>step 300, will finish Wed Mar 16 00:04:05 2011<br>step 400, will finish Wed Mar 16 00:03:37 2011 <br><br>
Step 460, time 0.92 (ps) LINCS WARNING<br>relative constraint deviation after LINCS: <br>rms 22.298270, max 137.226395 (between atoms 2136 and 2138)<br>bonds that rotated more than 30 degrees:<br> atom 1 atom 2 angle previous, current, constraint length<br>
2123 2124 92.6 0.1090 0.1866 0.1090 <br> 2139 2142 90.0 0.1090 9.1450 0.1090<br> 2139 2141 90.1 0.1090 9.2416 0.1090<br> 2139 2140 90.0 0.1090 9.1782 0.1090<br>
<br>
***********************************************************<br><br>Here is more details:<br><br>To diagnose the reason for crash I watched the trajectory and noticed the problem lies in hexane molecules and not the polymer. All LINCS and 1-4 warnings are because of hexane. So I followed the instruction on gmx site and simplified the problem. Topology is not the root cause since a 2 ns run on a single hexane works well. I am not getting any warnings before MD step so be ignored by maxwarn either. Regarding bad intial structure I should say that I was initially using emtol= 1000 and then I used 100 and the box is too big and molecules are far apart. (box is 20nm containing 110 hexane) <br>
<br>I also did PR where no error message come up. As I move on to MD NVT systems shows instabilities.<br><br>I dont know how else to overcome this situation which I have been working on nearly one week. <br><br><br>pbc = xyz <br>
;energygrps = PE HEX<br> <br>; Run control <br>integrator = md <br>dt = 0.002 <br>nsteps = 1000000 ;5000 <br>
nstcomm = 100 <br><br>; Output control<br>nstenergy = 100 <br>nstxout = 1 <br>nstvout = 0<br>nstfout = 0<br>
nstlog = 1000 <br>nstxtcout = 1000 <br><br>; Neighbor searching<br>nstlist = 10 <br>ns_type = grid <br><br>; Electrostatics/VdW <br>
coulombtype = PME <br>vdw-type = Shift <br>rcoulomb-switch = 0 <br>rvdw-switch = 0.9 ;0 <br><br>; Cut-offs<br>
rlist = 1.25 <br>rcoulomb = 1.25 ;1.1 <br>rvdw = 1.0 <br><br>; PME parameters<br>fourierspacing = 0.12 <br>fourier_nx = 0<br>
fourier_ny = 0<br>fourier_nz = 0<br>pme_order = 4 <br>ewald_rtol = 1e-5<br>optimize_fft = yes<br><br>; Temperature coupling <br>Tcoupl = v-rescale <br>
tc-grps = System ;HEX <br>tau_t = 0.1 ;0.1 <br>ref_t = 300 ;300 <br><br>; Pressure coupling<br>Pcoupl = no;Parrinello-Rahman <br>
Pcoupltype = isotropic <br>tau_p = 1 1 ;0.5 <br>compressibility = 4.5e-5 4.5e-5 <br>ref_p = 20 20 <br><br>; Velocity generation <br>
gen_vel = yes <br>gen_temp = 300.0 <br>gen_seed = 173529 <br><br>; Bonds<br>constraints = all-bonds ;<br>constraint-algorithm = lincs<br>
<br>; Free energy control stuff<br>free_energy = no;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><div class="gmail_quote"><br><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<div><br>
<br>
Moeed wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
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 <br>
</blockquote>
<br></div>
The manual will not describe every detail, but an understanding of the algorithms (through reading the appropriate literature) should provide you with what you need. Take Mark's advice and leave fourierspacing at its default value unless you are 100% sure of the effects of messing with it.<div>
<br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
electrostatics settings. BEfore that I had only vdw no run crashed. <br>
</blockquote>
<br></div>
That was a broken model, as we've discussed. Don't believe that its results are reliable.<div><br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Since I used to get LINCS warning I removed bond constraints but still <br>
</blockquote>
<br></div>
LINCS warnings don't mean you should turn off constraints. With a 2-fs timestep and an all-atom model, you absolutely need to be using constraints.<br>
<br>
<a href="http://www.gromacs.org/Documentation/Errors#LINCS.2fSETTLE.2fSHAKE_warnings" target="_blank">http://www.gromacs.org/Documentation/Errors#LINCS.2fSETTLE.2fSHAKE_warnings</a><div><br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
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>
</blockquote>
<br></div>
The best advice I can give has already been given:<br>
<br>
<a href="http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System" target="_blank">http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System</a><br>
<br>
Watch the trajectory. See what falls apart.<br>
<br>
You're also applying 70 bar of pressure to a system that may not yet be properly equilibrated for such conditions. I have found that the Parrinello-Rahman barostat is not particularly well-suited to harsh conditions, tight coupling, or simulations of any system that is far from equilibrium. You might be better off with Berendsen (and a fairly long tau_p) until your system stabilizes.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div><div></div><div>
<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>
<br>
<br>
Everything has a cause; nothing is accidental. No stable run should<br>
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.<br>
The proper term to analyze is Coul-recip, which corresponds to<br>
reciprocal space Coulombic term. I don't see that listed below.<br>
<br>
-Justin<br>
<br>
<br>
Thanks,<br>
Best,<br>
Moeed<br>
<br>
========================================<br>
step 164300, remaining runtime: 241 s step 164400,<br>
remaining runtime: 240 s step 164500, remaining<br>
runtime: 240 s step 164600, remaining runtime: 239<br>
s Warning: 1-4 interaction between 260 and 267 at<br>
distance 73679654.990 which is larger than the 1-4 table size<br>
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<br>
-0.0189929 -6.07777<br>
<br>
Coulomb-14 -186.509 15.9866 15.9529<br>
-0.0112174 -3.5896<br>
<br>
LJ (SR) -2691.84 117.026 107.231<br>
-0.507373 -162.361<br>
<br>
Coulomb (SR) 725.662 17.6483 17.5876<br>
0.0158275 5.06483<br>
<br>
fourierspacing = 0.3<br>
<br>
<br>
LJ-14 757.129 26.4936 26.4578<br>
-0.0149128 -4.77214<br>
<br>
Coulomb-14 -199.523 14.949 14.158<br>
-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<br>
0.0521352 16.6834<br>
<br>
====================================================<br>
pbc = xyz ; Run control integrator = md dt = 0.002 nsteps = 1000000 ;5000 nstcomm = 100 ; Output control<br>
nstenergy = 100 nstxout = 100 nstvout = 0<br>
nstfout = 0<br>
nstlog = 1000 nstxtcout =<br>
1000 ; Neighbor searching<br>
nstlist = 10 ns_type =<br>
grid ; Electrostatics/VdW<br>
coulombtype = PME vdw-type = Shift rcoulomb-switch = 0 rvdw-switch = 0.9 ;0 ; Cut-offs<br>
rlist = 1.25 rcoulomb = 1.25 ;1.1 rvdw = 1.0 ; 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<br>
tc-grps = System ;HEX tau_t = 0.1 ;0.1 ref_t = 400 ;300 ; 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 ; Velocity generation gen_vel =<br>
yes gen_temp = 300.0 gen_seed = 173529 ; Bonds<br>
constraints = all-bonds constraint-algorithm = lincs<br>
<br>
<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></div></div>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> <<a href="http://vt.edu" target="_blank">http://vt.edu</a>> | (540) 231-9080<div><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>
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<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" target="_blank">http://mmrg.chemeng.mcgill.ca/pages/current-group-members/moeed-shahamat.php</a><br>
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-- <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>
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