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

[Rama]

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"

-----------.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.