[gmx-users] Fwd: error in running md.mdp

[VARSHA RANI]

---------- Forwarded message ----------
From: VARSHA RANI <varsha24_sps at jnu.ac.in>
Date: Mon, Jun 12, 2017 at 11:24 PM
Subject: Re: [gmx-users] error in running md.mdp
To: chauhan harish chandr <harishcc02901 at gmail.com>


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.*

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




On Mon, Jun 12, 2017 at 9:38 PM, VARSHA RANI <varsha24_sps at jnu.ac.in> wrote:

>
> ---------- Forwarded message ----------
> From: Justin Lemkul <jalemkul at vt.edu>
> Date: Mon, Jun 12, 2017 at 6:50 PM
> Subject: Re: [gmx-users] error in running md.mdp
> To: gmx-users at gromacs.org
>
>
>
>
> On 6/12/17 9:14 AM, VARSHA RANI wrote:
>
>> Hi all,
>> I am running molecular dynamics for organic molecules without any solvent
>> using "GROMACS-5.0.7".  Initial steps ran fine till npt.mdp. But while
>> running mdrun after gompp using md.mdp, I got the following error:
>>
>>
>> Fatal error
>> " Not enough memory. Failed to allocate 2289030720 aligned elements of
>> size
>> 4 for grid->grid.
>>
>> My system contains 3456 atoms and computer has sufficient memory of 300
>> GB.
>> md.log file is also attached here.
>>
>> Any help will be appreciable.
>>
>>
> You need to provide your full grompp command, the screen output, and the
> text of the .mdp file.
>
> -Justin
>
> --
> ==================================================
>
> 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
>
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