[gmx-users] Abnormal alignment of waters after NVT simulation

[Mark Abraham]

On 8/08/2012 5:58 PM, Du Jiangfeng (BIOCH) wrote:
> Dear All,
>
> I encountered a very weird result after performing NVT simulation, all the waters aligned in lines, and they look like crystal cells.

If they're in geometric lines, then you're probably looking at your 
input configuration. If they're just close to being in lines, you've 
probably used position restraints on them. Compare how they look with 
other Martini simulations, e.g. from tutorials.

Mark

>   How did it turn out like this by temperature coupling? The following is the nvt.mdp parameters:
>
> ; NVT equilibration
> define		= -DPOSRES	; position restrain the protein but free the waters and lipids
> ; Run parameters
> integrator	= md		; leap-frog integrator
> nsteps		= 120000		; 0.025 * 120000 = 3 ns
> dt		= 0.025		; 25 fs since this is coarse grained system with martini force field
> ; Output control
> nstxout		= 100		; save coordinates every 2.5 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	= yes		; first dynamics run
> constraint_algorithm = LINCS	; holonomic constraints
> constraints	= none	; I suppose "none" is standard used in martini force field
> lincs_iter	= 1		; accuracy of LINCS
> lincs_order	= 4		; also related to accuracy
> lincs_warnangle          = 30
> ; Neighborsearching
> ns_type		= grid		; search neighboring grid cells
> nstlist		= 10		; 250 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	= 0.12		; grid spacing for FFT
> ; Temperature coupling is on
> tcoupl		= berendsen	; modified Berendsen thermostat
> tc-grps		= Protein Non-Protein	; two coupling groups - more accurate
> tau_t		= 0.2	0.2	; time constant, in ps
> ref_t		= 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
>   
>
> Which parameters should be blamed to cause such artificial result?
>
> Thank you!
>
>      Jiangfeng Du, PhD Student
>      Cardiovascular Research Institute Maastricht
>      Department of Biochemistry
>      P.O. Box 616
>      Mobile: +31-681741859
>      FAX: +31-43-3884159
>      6200 MD Maastricht
>      The Netherlands--
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