[gmx-users] Re: number of degrees of frredom
Vitaly Chaban
vvchaban at gmail.com
Mon Jul 12 17:55:37 CEST 2010
So cite the error please. I did not find the error regarding degrees
of freedom below.
Do you want to keep your PE in vacuum?
Dr. Vitaly Chaban
> 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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