[gmx-users] number of degrees of frredom

[Moeed]

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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