[gmx-users] Unusual Blow up

[Nima Soltani]

Justin Lemkul <jalemkul at ...> writes:

> 
> 
> On 9/1/15 9:40 AM, Nima Soltani wrote:
> > Hi everyone
> > I am simulating the interactions between a small peptide and different
> > metallic surfaces solvated in TIP3P water.
> > So far i have simulated  3 different surfaces correctly , however the last
> > surface becames unstable after nearly 2 ns of simulation.
> > I did an EM step again and reduced time step to half (i.e. 0.5 fs) however
> > it didn't work ... I've even set lincs-warnangle to its maximum value(=
> > 90), howeer it failed again . I don't have any idea how to fix it
> >
> > The surface is Polarizable by using *Drude* oscillators and i think these
> > oscillatoras are the cause of problems .
> >
> >
> >     Step           Time         Lambda
> >          2270000     2270.00000        0.00000
> >
> >     Energies (kJ/mol)
> >              U-B    Proper Dih.  Improper Dih.      CMAP Dih.          LJ-14
> >      3.87510e+02    6.15054e+01    1.98057e+01   -5.57740e+01    6.96654e+01
> >       Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
> >      2.93372e+03    8.97847e+04   -6.19085e+03   -7.47168e+05    2.44969e+03
> >     COM Pull En.      Potential    Kinetic En.   Total Energy    Temperature
> >      1.39457e-03   -6.57708e+05    1.23026e+05   -5.34682e+05    3.09198e+02
> >   Pres. DC (bar) Pressure (bar)   Constr. rmsd
> >     -2.03445e+02   -9.16454e+01    1.80260e-06
> >
> >
> > -------------------------------------------------------
> > Program gmx, VERSION 5.0.5
> > Source code file:
> > /share/apps/gromacs-5.0.5/gromacs-5.0.5/src/gromacs/mdlib/constr.c, line:
> > 224
> >
> > Fatal error:
> > Too many LINCS warnings (1000)
> > If you know what you are doing you can adjust the lincs warning threshold
> > in your mdp file
> > or set the environment variable GMX_MAXCONSTRWARN to -1,
> > but normally it is better to fix the problem
> > For more information and tips for troubleshooting, please check the GROMACS
> > website at http://www.gromacs.org/Documentation/Errors
> > -------------------------------------------------------
> >   Thanks in advance for any suggestions / assistance
> >
> 
> You'll have to describe in exact detail what you're doing.  It's very easy to 
> break a polarizable model.  What are the sources of the parameters?  Have
these 
> parameters been validated in the context of TIP3P?  This sounds like a very 
> weird combination to me, to have part of the system polarizable and the
rest not.
> 
> -Justin
> 
I am simulating a peptide near these interfaces and every step of preparing
my input files was carefully tested (either by me or by computer :-) )
i am applying a 310K temperature to Drude oscillating particles of the
silver ( and Au), while the rest of metal atom types have been frozen. 
every time the simulation breaks , one oscillator in the metal is moving so
fast that it changes it;s angle more than 90 degree !

details of simulation is in the mdp file 
; Run parameters
integrator	= md		; leap-frog integrator
nsteps		= 10000000		; 10 ns 
dt		    = 0.001		; 1 fs
;Freeze groups
freezegrps 	= GolPFreeze
freezedim	= Y Y Y
; Output control
nstxout-compressed             = 0
nstxout		= 10000		; save coordinates every 10 ps
nstvout		= 10000		; save velocities every 10 ps
nstenergy	= 10000		; save energies every 10 ps
nstlog		= 10000		; update log file every 10 ps
; Bond parameters
constraint_algorithm    = lincs	    ;
constraints	            = all-bonds	; 
; Neighborsearching
cutoff_scheme   = Verlet
ns_type		    = grid		; 
nstlist		    = 30	    	; 
rcoulomb	    = 1.2		; 
rvdw		    = 1.2		;  
; Electrostatics
coulombtype	    = PME		; 
pme_order	    = 4		    
fourierspacing	= 0.16		; grid spacing for FFT
; Temperature coupling is on
tcoupl		= Nose-Hoover	            ; Nose-Hoover thermostat
tc-grps		= Protein Water_and_ions GoldnotFrz GolPFreeze	;
tau_t		= 0.5	  0.5		 0.5		0.5	; 
ref_t		= 310 	  310		 310		0	; 
; Pressure coupling is on
pcoupl		        = Parrinello-Rahman	    
pcoupltype	        = semiisotropic	           tau_p		        = 1.0		            
ref_p		        = 1.0	     1.0	    
compressibility     	= 0        4.5e-5         
refcoord_scaling    = com 	
; Periodic boundary conditions
pbc		= xyz		; 3-D PBC
; Dispersion correction
DispCorr	= EnerPres	; account for cut-off vdW scheme
; Velocity generation
gen_vel		= no		; Velocity generation is off 
; Pull code
pull            = umbrella
pull_geometry   = distance  ; simple distance increase 
pull_dim        = N N Y
pull_start      = yes       ; define initial COM distance > 0
pull_ncoords    = 1
pull_ngroups    = 2
pull_coord1_groups    = 1 2
pull_group1_name     = Ref 
pull_group2_name     = Protein 
pull_coord1_rate      = 0     
pull_coord1_k         = 1000      ; kJ mol^-1 nm^-2
pull-coord1-init	=0
pull_nstxout    	= 500      ; every 0.5 ps
pull_nstfout    	= 500      ; every 0.5 ps