[gmx-users] error in running md.mdp

[Justin Lemkul]

On 6/12/17 2:58 PM, VARSHA RANI wrote:
> Thanks for the reply.  Grompp command is like that:-
> 
> "gmx grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -o md_0_1.tpr"
> 
> 
> It completed successfully. Then I ran
> 
> "gmx mdrun -deffnm md_0_1"
> 
> and I got output on screen like this
> 
> *Fatal error
> *>* " Not enough memory. Failed to allocate 2289030720 aligned elements of size
> *>* 4 for grid->grid.*
> 

Your system is blowing up and the grid is becoming infinite.  See below.

> (called from /home/harish/gromacs-5.0.7/src/gromacs/utility/smalloc.cpp/)
> 
> 
> And md.mdp is also given below...
> 
> 
> title		= penta-simulaiton
> ; Run parameters
> integrator	= md		; leap-frog integrator
> nsteps		= 100000	; 2 * 100000 = 200 ps (1 ns)
> dt		    = 0.002		; 2 fs
> ; Output control
> nstxout		        = 5000		; save coordinates every 1.0 ps
> nstvout		        = 5000		; save velocities every 1.0 ps
> nstenergy	        = 5000		; save energies every 1.0 ps
> nstlog		        = 5000		; update log file every 1.0 ps
> nstxout-compressed  = 5000      ; save compressed coordinates every 1.0 ps
>                                  ; nstxout-compressed replaces nstxtcout
> compressed-x-grps   = System    ; replaces xtc-grps
> ; Bond parameters
> continuation	        = yes		; Restarting after NPT
> constraint_algorithm    = lincs	    ; holonomic constraints
> constraints	            = all-bonds	; all bonds (even heavy atom-H
> bonds) constrained
> lincs_iter	            = 1		    ; accuracy of LINCS
> lincs_order	            = 4		    ; also related to accuracy
> ; Neighborsearching
> cutoff-scheme   = Verlet
> ns_type		    = grid		; search neighboring grid cells
> nstlist		    = 10	        ; 20 fs, largely irrelevant with Verlet scheme
> rlist		    = 2
> rcoulomb	    = 1.5		; short-range electrostatic cutoff (in nm)
> rvdw		    = 1.5		; short-range van der Waals cutoff (in nm)

Where did you get these cutoff values?  They don't look like anything a normal 
force field uses.

> ; Electrostatics
> coulombtype	    = PME		; Particle Mesh Ewald for long-range electrostatics
> pme_order	    = 5		    ; cubic interpolation

Fifth order?  Try 4.

-Justin

> fourierspacing	= 0.16		; grid spacing for FFT
> ; Temperature coupling is on
> tcoupl		= V-rescale	            ; modified Berendsen thermostat
> tc-grps		= Molecule  	; two coupling groups - more accurate
> tau_t		= 0.1	  	        ; time constant, in ps
> ref_t		= 300 	 	        ; reference temperature, one for each group, in K
> ; Pressure coupling is on
> pcoupl		        = Parrinello-Rahman	    ; Pressure coupling on in NPT
> pcoupltype	        = isotropic	            ; uniform scaling of box vectors
> tau_p		        = 2.0		            ; time constant, in ps
> ref_p		        = 1.0		            ; reference pressure, in bar
> compressibility     = 4.5e-5	            ; isothermal compressibility
> of water, bar^-1
> ; 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
> 

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

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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

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