[gmx-users] NVT problem

[Andres Ortega Guerrero]

Thank you Justin for Your Help, and advice, i have already the modification on the nvt.mdp that you suggest,  but the problem is still there, my system has about 150.000 atoms , and for the energy minization i used DFLEXIBLE, and  emtol was ajusted to 1000, i take a look to the steep0.pdb that gromacs produce, and there are atoms out of the box, but the DOX molecule is OK 

what would you suggest?
- a emtol lower?
- a water and dox md? ( maybe the DOX.itp can be the problem) ?

Thank you Justin, 

Andres 


> Date: Sat, 15 Mar 2014 14:23:15 -0400
> From: jalemkul at vt.edu
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] NVT problem
> 
> 
> 
> 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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