Moeed wrote:
Hello Justin,
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
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.
electrostatics settings. BEfore that I had only vdw no run crashed.
That was a broken model, as we've discussed. Don't believe that its results are
reliable.
Since I used to get LINCS warning I removed bond constraints but still
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.
http://www.gromacs.org/Documentation/Errors#LINCS.2fSETTLE.2fSHAKE_warnings
system is showing instabilities. I am confident that topology is fine
and just wondering how else one can inspect root cause for unphysical
forces.
The best advice I can give has already been given:
http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System
Watch the trajectory. See what falls apart.
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.
-Justin
fourierspacing =0.12 : Coul. recip. 636.217
8.69433 8.62908 0.0167398 3.68278
fourierspacing =0.3 : Coul. recip. 642.921
6.06063 6.02832 -0.00984063 -2.16496
Everything has a cause; nothing is accidental. No stable run should
ever show LINCS warnings like this, so yes, there is something to fix.
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.
-Justin
Thanks,
Best,
Moeed
========================================
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
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size
=========================================
results till t=320 ps (before first run crash)
fourierspacing = 0.12
LJ-14 757.246 26.6239 26.5661
-0.0189929 -6.07777
Coulomb-14 -186.509 15.9866 15.9529
-0.0112174 -3.5896
LJ (SR) -2691.84 117.026 107.231
-0.507373 -162.361
Coulomb (SR) 725.662 17.6483 17.5876
0.0158275 5.06483
fourierspacing = 0.3
LJ-14 757.129 26.4936 26.4578
-0.0149128 -4.77214
Coulomb-14 -199.523 14.949 14.158
-0.0519427 -16.6218
LJ (SR) -2670.5 111.201 109.688
0.19784 63.3092
Coulomb (SR) 739.794 16.1807 15.4473
0.0521352 16.6834
====================================================
pbc = xyz
; Run control integrator
= md dt = 0.002
nsteps = 1000000 ;5000 nstcomm
= 100
; Output control
nstenergy = 100 nstxout
= 100 nstvout = 0
nstfout = 0
nstlog = 1000 nstxtcout =
1000
; Neighbor searching
nstlist = 10 ns_type =
grid
; Electrostatics/VdW
coulombtype = PME vdw-type
= Shift rcoulomb-switch = 0
rvdw-switch = 0.9 ;0
; Cut-offs
rlist = 1.25 rcoulomb
= 1.25 ;1.1 rvdw = 1.0
; PME parameters
fourierspacing = 0.3 fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 4 ewald_rtol = 1e-5
optimize_fft = yes
; Temperature coupling Tcoupl = v-rescale
tc-grps = System ;HEX
tau_t = 0.1 ;0.1 ref_t
= 400 ;300
; Pressure coupling
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 =
yes gen_temp = 300.0
gen_seed = 173529
; Bonds
constraints = all-bonds
constraint-algorithm = lincs
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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--
Moeed Shahamat
Graduate Student (Materials Modeling Research Group)
McGill University- Department of Chemical Engineering
Montreal, Quebec H3A 2B2, Canada
Web:http://mmrg.chemeng.mcgill.ca/pages/current-group-members/moeed-shahamat.php
Web:http://mmrg.chemeng.mcgill.ca/
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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