Moeed wrote:
Hi everyone,
My attempt to conduct a NPT failed although everything seemed to be
going well. Topology is OK and I am just curious why system is blowing
up all of a sudden towards the end of simulation. I should mention that
by changing fourierspacing from 0.12 to 0.3 everything works fine till
the end of run and comparison between energy terms (up until the crash
point) shows very slight difference between two runs ( less than 2% even
for electrostatic terms). I am aware that blowing up is due to
unphysical forces but is this happening by accidient or there is an
underlying reason I should take care of.
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 | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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