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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