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
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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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
==================================================
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