[gmx-users] problem with tutorial KALP-15 in DPPC

[Justin Lemkul]

On 2/3/14, 12:10 PM, serena wrote:
> Hi all
> I'm doing the GROMACS tutorial KALP-15 in DPPC. I've done the steps until
> the energy minimization, so now I've my system at an energy minimum and  I'm
> doing the equilibration with this nvt.mdp:
>
> define		= -DPOSRES  ; position restrain the protein and lipid
> ; Run parameters
> integrator	= md		; leap-frog integrator
> nsteps		= 50000		; 2 * 50000 = 100 ps
> dt		= 0.002		; 2 fs
> ; Output control
> nstxout		= 100		; save coordinates every 0.2 ps
> nstvout		= 100		; save velocities every 0.2 ps
> nstenergy	        = 100		; save energies every 0.2 ps
> nstlog		= 100		; update log file every 0.2 ps
> ; Bond parameters
> continuation	 = no		        ; first dynamics run
>   constraint_algorithm = lincs	; holonomic constraints
>   constraints	= h-bonds	        ; vecchio all bonds (even heavy atom-H bonds)
> constrained
>   lincs_iter	= 1		            ; accuracy of LINCS
>   lincs_order	= 4		            ; also related to accuracy
> ; Neighborsearching
> ns_type		= grid		; search neighboring grid cels
> nstlist		= 5		    ; 10 fs
> rlist		= 1.2		; vecchio: 1.0 short-range neighborlist cutoff (in nm)
> rcoulomb	= 1.2 		; short-range electrostatic cutoff (in nm)
> rvdw		= 1.2		; short-range van der Waals cutoff (in nm)
> ; Electrostatics
> coulombtype	= PME 		; Particle Mesh Ewald for long-range electrostat
> pme_order	= 4		    ; cubic interpolation
> fourierspacing	= 0.16		; grid spacing for FFT
> ; Temperature coupling is on
> tcoupl		= V-rescale	            ; modified Berendsen thermostat
> tc-grps		= Protein DPPC SOL_CL	; three coupling groups - more accurate
> tau_t		= 0.1	0.1	0.1	        ; time constant, in ps
> ref_t		= 323 	323	323	        ; reference temperature, one for each group,
> in K
> ; Pressure coupling is off
> pcoupl		= no 		; no pressure coupling in NVT
> ; Periodic boundary conditions
> pbc		    = xyz		; 3-D PBC
> ; Dispersion correction
>   DispCorr	= EnerPres	; account for cut-off vdW scheme
> ; Velocity generation
> gen_vel		= yes		; assign velocities from Maxwell distribution
> gen_temp	= 323		; temperature for Maxwell distribution
> gen_seed	= -1		; generate a random seed
> ; COM motion removal
> ; These options remove motion of the protein/bilayer relative to the
> solvent/ions
> nstcomm		= 1
> comm-mode	= Linear
> comm-grps	= Protein_DPPC SOL_CL
>
> I've done this command:
> grompp -f nvt.mdp -c em.gro -p topol.top -n index.ndx -o nvt.tpr
> mdrun -deffnm nvt
>
> but I received this error:
> starting mdrun 'Protein in water'
> 50000 steps,    100.0 ps.
>
> step 0: Water molecule starting at atom 101831 can not be settled.
> Check for bad contacts and/or reduce the timestep if appropriate.
>
> step 0: Water molecule starting at atom 99524 can not be settled.
> Check for bad contacts and/or reduce the timestep if appropriate.
> Wrote pdb files with previous and current coordinates
> Wrote pdb files with previous and current coordinates
>
> Fatal error:
> 1 particles communicated to PME node 8 are more than 2/3 times the cut-off
> out of the domain decomposition cell of their charge group in dimension x.
> This usually means that your system is not well equilibrated.
>
> What means of this error? How to fix it?

Energy minimization wasn't adequate, so there are bad contacts upon initiating 
MD.  I don't know why this would have happened in the case of the tutorial 
system if the initial configuration was built correctly.  Examine the output of 
EM and scrutinize the atoms indicated above in the starting configuration for 
bad contacts and their source(s).

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================