rama david wrote:
Hi Gromacs Specialist,
Thank you Justin For your reply.
I run one Simulated Annealing) MD after your reply.
My aim is to find protein conformation and study protein
self assembly study ..
the protocol I follow is as..
1. Upto energy minimisation I followed the general way
2. I did nvt at 277 K(position resstrain)
3. I did npt at 277 k ((Position Restrain )
4. then I did the SA (I removed Position Restrain ) with following mdp
title = simulated run
integrator = md ; md integrator
tinit = 0 ; [ps] starting time for run
dt = 0.002 ; [ps] time step for integration
nsteps = 5000000 ; maximum number of steps to
integrate, 0.002 * 5000000 10 ns
comm_mode = Linear ; remove center of mass translation
comm_grps = Protein Non-Protein ; group(s) for center of mass
motion removal
; 7.3.8 Output Control
nstxout = 100 ; [steps] freq to write
coordinates to trajectory
nstvout = 100 ; [steps] freq to write velocities
to trajectory
nstfout = 100 ; [steps] freq to write forces to trajectory
nstlog = 100 ; [steps] freq to write
energies to log file
nstenergy = 100 ; [steps] freq to write
energies to energy file
nstxtcout = 500 ; [steps] freq to write
coordinates to xtc trajectory
xtc_precision = 100 ; [real] precision to write xtc
trajectory
xtc_grps = System ; group(s) to write to xtc trajectory
energygrps = System ; group(s) to write to energy file
; 7.3.9 Neighbor Searching
nstlist = 5 ; [steps] freq to update neighbor list
ns_type = grid ; method of updating neighbor list
pbc = xyz ; periodic boundary conditions
in all directions
rlist = 1.0 ; [nm] cut-off distance for
the short-range neighbor list
; 7.3.10 Electrostatics
coulombtype = PME ; Particle-Mesh Ewald electrostatics
rcoulomb = 1.0 ; [nm] distance for Coulomb cut-off
; 7.3.11 VdW
vdwtype = cut-off ; twin-range cut-off with
rlist where rvdw >= rlist
rvdw = 1.4 ; [nm] distance for LJ cut-off
DispCorr = EnerPres ; apply long range dispersion
corrections for energy
; 7.3.13 Ewald
fourierspacing = 0.16 ; [nm] grid spacing for FFT
grid when using PME
pme_order = 4 ; interpolation order for PME, 4 = cubic
ewald_rtol = 1e-5 ; relative strength of
Ewald-shifted potential at rcoulomb
; 7.3.14 Temperature Coupling
tcoupl = berendson ;
tc_grps = Protein Non-Protein ; groups to
couple seperately to temperature bath
tau_t = 0.1 0.1 ; [ps] time
constant for coupling
ref_t = 277 277 ; [K] reference
temperature for coupling
annealing = single single
annealing_npoint = 2 2
annealing_time = 0 50 0 50
annealing_temp = 277 333 277 300
; 7.3.15 Pressure Coupling
pcoupl = Parrinello-Rahman ;
pcoupltype = isotropic ; pressure
coupling in x-y-z directions
tau_p = 2.0 ; [ps]
time constant for coupling
compressibility = 4.5e-5 ; [bar^-1]
compressibility
ref_p = 1.0 ; [bar]
reference pressure for coupling
; 7.3.17 Velocity Generation
gen_vel = no ; velocity generation turned off
gen_temp = 277
; 7.3.18 Bonds
constraints = all-bonds ; convert all bonds to constraints
constraint_algorithm = LINCS ; LINear Constraint Solver
continuation = yes ; apply constraints to the
start configuration
lincs_order = 4 ; highest order in the
expansion of the contraint coupling matrix
lincs_iter = 1 ; number of iterations to
correct for rotational lengthening
lincs_warnangle = 30 ; [degrees] maximum angle that
a bond can rotate before LINCS will complain
continuation =yes
so my Queries are
1. As I not define = -DPOSRES in SA mdp is it sound well???,
should I have to run Production run after my
SA run(That means Is SA is substitute to Production run ??)
??? or I have to use define = -DPOSRES in my SA mdp ,
and then I have to do production run
2. Or as per Justin recommendation NVT at 277 ,followed by SA
(Then I have to use define = -DPOSRES in My SA mdp file ,Is it right??)
then NPT afterward Production run ..
So what is your suggestion ???
The answers to your question depend entirely upon what you want to do and
observe. If you're using SA simply as part of an equilibration protocol (as I
often do, which was what I based my suggestion upon earlier), then I stick with
my protocol, which is point #2.
If you're trying to model the behavior of your system in response to a change in
termperature, then SA is your production run and you would not use position
restraints.
It is still not clear to me how you wish to use SA or what you hope to observe
from it, so that's the best I can offer.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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