[gmx-users] NVT problem

[Justin Lemkul]

On 3/15/14, 2:19 PM, Andres Ortega wrote:
> HI , Dear Gromacs Users,
>
> I´ve been trying to run a NVT simulation, in order to equilibrate my system(
> POPC + IONCHANNEL + SOL_IONS and DOX( Drug Molecule), i have already run a
> EM, with DFLEXIBLE, and when i´m trying to run the NVT.mdp, the usual
> comment of Water cannot be settle appear
>
> and this
>
> Step 1, time 0.002 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 417295953701.842102, max 94388491386880.000000 (between atoms 7122 and
> 7123)
> bonds that rotated more than 30 degrees:
>
> according with previous post, this could be of a problem of the topol (DOX)
> or problems with my mdp file, this is my .mdp , i was wondering if you could
> help me and give me some advices to solve this
>
> Thanks in advance for your time and attention , Andres Ortega
>
> title		= NVT equilibration for channel_dox
> define		= -DPOSRES -DPOSRES_DOX	; position restrain the protein and for DOX
> ; Run parameters
> integrator	= md		; leap-frog integrator
> nsteps		= 5000000	; 2 * 500000 = 1 ns ;10ns
> dt		    = 0.002		; 2 fs
>
> cutoff-scheme = verlet   ;
>
> ; Output control
> nstxout		= 1000		; save coordinates every 2 ps
> nstvout		= 1000		; save velocities every 2 ps
> nstenergy	= 1000		; save energies every 2 ps
> nstlog		= 1000		; update log file every 2 ps
>
> ; Bond parameters
> continuation	= no		    ; first dynamics run
> 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
> ns_type		= grid		; search neighboring grid cels
> nstlist		= 10		    ; 10 fs
> rlist		= 1.2		; 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 electrostatics
> 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 POPC DOX Water_and_ions 	; three coupling groups - more
> accurate
> tau_t		= 0.1	0.1		0.1   0.1        ; time constant, in ps
> ref_t		= 310 	310		310   310	        ; 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	= 310		; 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_POPC DOX Water_and_ions
>

Specifying DOX as separately in both tc-grps and comm-grps is the most probable 
source of error.  It is too small to justify its own thermostat, and certainly 
should not have its COM motion removed separately.

-Justin

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

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

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