[gmx-users] Re: Change in the position of structural Zinc and calcium ions during MD

[Justin Lemkul]

On 11/12/13 1:47 PM, Rama wrote:
> Hi Justin,
>
> Below I pasted .mdp file and topology. In .log file I could see energy term
> for position restraints.
>
> ------------.mdp file-----------
> title		= NPT Equilibration
> define		= -DPOSRES	; position restraints for protein
> ; Run parameters
> integrator	= md		; leap-frog integrator
> nsteps		= 500000	; 2 * 500000 = 1000 ps (1 ns)
> dt		    = 0.002		; 2 fs
> ; Output control
> nstxout		= 500		; save coordinates every 1 ps
> nstvout		= 500		; save velocities every 1 ps
> nstenergy	= 500		; save energies every 1 ps
> nstlog		= 500		; update log file every 1 ps
> ; Bond parameters
> continuation	= yes		    ; Restarting after NVT
> 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		= 5		    ; 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		= Nose-Hoover		    ; More accurate thermostat
> tc-grps		=  Protein_CA_ZN   DMPC   SOL_CL	; three coupling groups - more
> accurate
> tau_t		=       0.5	   0.5 	   0.5	        ; time constant, in ps
> ref_t		=       298 	   298	   310	        ; reference temperature, one for
> each group, in K
> ; Pressure coupling is on
> pcoupl		= Parrinello-Rahman	    ; Pressure coupling on in NPT
> pcoupltype	= semiisotropic		    ; uniform scaling of x-y box vectors,
> independent z
> tau_p		= 5.0			        ; time constant, in ps
> ref_p		= 1.0	1.0		        ; reference pressure, x-y, z (in bar)
> compressibility = 4.5e-5	4.5e-5	; isothermal compressibility, 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
> ; COM motion removal
> ; These options remove motion of the protein/bilayer relative to the
> solvent/ions
> nstcomm         = 1
> comm-mode       = Linear
> comm-grps       = Protein_DMPC SOL_CL
> ; Scale COM of reference coordinates
> refcoord_scaling = com
>
>
> ------------topol.top------------
> ; Include Position restraint file
> #ifdef POSRES
> #include "posre.itp"
> #endif
>
> ; Strong position restraints for InflateGRO
> #ifdef STRONG_POSRES
> #include "strong_posre.itp"
> #endif
>
> ; Include DMPC topology
>   #include "rama4LJ.ff/dmpcLJ.itp"
>
> ; Include water topology
> #include "rama4LJ.ff/spc.itp"
>
> #ifdef POSRES_WATER
> ; Position restraint for each water oxygen
> [ position_restraints ]
> ;  i funct       fcx        fcy        fcz
>     1    1       1000       1000       1000
> #endif
>
> ; Include topology for ions
> #include "rama4LJ.ff/ions.itp"
>

Do you have appropriate [position_restraints] assigned in this topology?  None 
of the above, as shown, pertains to the ions, and the only relevant #ifdef block 
that would be triggered by -DPOSRES is for the protein.

-Justin

> -----------.log file------------
>     Energies (kJ/mol)
>            Angle    Proper Dih. Ryckaert-Bell.  Improper Dih.          LJ-14
>      1.77761e+04    3.10548e+03    7.97673e+03    4.40586e+02    8.14131e+03
>       Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
>      2.59758e+04    2.74092e+04   -2.56846e+03   -4.68637e+05   -1.67418e+05
>   Position Rest.      Potential    Kinetic En.   Total Energy    Temperature
>      7.09403e+02   -5.47088e+05    8.83115e+04   -4.58777e+05    3.07118e+02
>   Pres. DC (bar) Pressure (bar)   Constr. rmsd
>     -2.00493e+02    1.00080e+00    0.00000e+00
>
>
> Thanks
>
> --
> View this message in context: http://gromacs.5086.x6.nabble.com/Change-in-the-positon-of-structural-Zinc-and-calcium-ions-during-MD-tp5012467p5012474.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
>

-- 
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Justin A. Lemkul, Ph.D.
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

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