[gmx-users] number of degrees of frredom
Moeed
lecielll at googlemail.com
Mon Jul 12 17:37:57 CEST 2010
Dear Justin,
The actual box I got by replicating monomer units has size of 15 0.5 0.5!!!!
That is chain has no space to move. I know you have already given me some
tips on high repulsion in the system but that had to do with incorrect
topology file. I assure you I have learned a lot from your tips ;)
This time I need to have such packed system because that gives me the
density I want. 0.9g/cm3 for PE! for a chain of 60 ethylene units the size
should be identical to the actual size 15 0.5 0.5. And I am wondering how
can I work with much longer chains ( 20 times longer)...
md grompp is giving error about degrees of freedom. Any advise on this in
appreciated...
Thank you,
md
grompp****************************************************************************
aking dummy/rest group for Acceleration containing 2896 elements
Making dummy/rest group for Freeze containing 2896 elements
Making dummy/rest group for Energy Mon. containing 2896 elements
Making dummy/rest group for VCM containing 2896 elements
Number of degrees of freedom in T-Coupling group Eth is 5373.22
Number of degrees of freedom in T-Coupling group EthB is 211.89
Number of degrees of freedom in T-Coupling group EthE is 211.89
Making dummy/rest group for User1 containing 2896 elements
Making dummy/rest group for User2 containing 2896 elements
Making dummy/rest group for XTC containing 2896 elements
Making dummy/rest group for Or. Res. Fit containing 2896 elements
Making dummy/rest group for QMMM containing 2896 elements
T-Coupling has 3 element(s): Eth EthB EthE
Energy Mon. has 1 element(s): rest
Acceleration has 1 element(s): rest
Freeze has 1 element(s): rest
User1 has 1 element(s): rest
User2 has 1 element(s): rest
VCM has 1 element(s): rest
XTC has 1 element(s): rest
Or. Res. Fit has 1 element(s): rest
QMMM has 1 element(s): rest
mdpfile**************************************************************************************
title = PE-Hexane
;define = -DPOSRES ; tells gromacs to perform position
restrained dynamics/include posre.itp into topology used for position
restraint
pbc = xyz ; use priodic BCs in all
directions
; Run control
integrator = md ; type of dynamics algorithm. Here
md uses a leap-frog algorithm for integrating Newtons's eq of motion
dt = 0.002 ; in ps !
nsteps = 5000 ; length of simulation= nsteps*dt
nstcomm = 1 ; frequency for center of mass
motion removal
; Output control
nstenergy = 100 ; frequency to write energies to
energy file. i.e., energies and other statistical data are stored every 10
steps
nstxout = 100 ; frequency to write
coordinates/velocity/force to output trajectory file. how often snapshots
are collected= nstxout*dt
nstvout = 100
nstfout = 0
nstlog = 100 ; frequency to write energies to log
file
nstxtcout = 10 ; frequency to write coordinates to
xtc trajectory
; Neighbor searching
nstlist = 10 ; frequency to update neighbor list.
Neighborlist will be updated at least every 10 steps. Manual p80
ns_type = grid ; make a grid in the box and only
check atoms in neighboring grid cells when constructing a new neighbor list
every nstlist steps
; Electrostatics/VdW
coulombtype = Shift ; tells gromacs how to model
electrostatics. Coulomb/LJ potential is decreased over the whole range and
forces decay smoothly to zero betw$
vdw-type = Shift ; rcoulomb-switch/rvw-switch &
rcoulomb/rvdw
rcoulomb-switch = 0 ; where to start switching the
Coulomb potential
rvw-switch = 0 ; where to start switching the LJ
potential
; Cut-offs
rlist = 1.1 ; in nm. Cut-off distance for
short-range neighbor list
rcoulomb = 1.0 ; distance for coulomb cut-off
rvdw = 1.0 ; distance for coulomb cut-off
; Temperature coupling
Tcoupl = berendsen
tc-grps = Eth EthB EthE ;HEX ; groups to couple
to thermostat; Berendsen temperature coupling is on in these groups
tau_t = 0.1 0.1 0.1 ;0.1 ; time constant for
T coupling
ref_t = 300 300 300 ;300 ; reference T for
coupling. When you alter the T, don't forget to change the gen_temp for
velocity generation
; Pressure coupling
Pcoupl = berendsen ; Pressure coupling is not on
Pcoupltype = isotropic ; means the box expands and
contracts in all directions (x,y,z) in order to maintain the proper pressure
tau_p = 0.5 ; time constant for coupling in ps
compressibility = 4.5e-5 ; compressibility of solvent used in
simulation in 1/bar
ref_p = 1.0 ; reference P for coupling in bar
; Velocity generation Generate velocites is on at 300 K.
Manual p155
gen_vel = yes ; generate velocites according to
Maxwell distribution at T: gen_temp with random gen seed gen_seed
gen_temp = 300.0 ; T for Maxwell distribution
gen_seed = 173529 ; used to initialize random
generator for random velocities
; Bonds
constraints = all-bonds ; sets the LINCS constraint for all
bonds
constraint-algorithm = lincs
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