Dear Justin,<br><br>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 ;) <br>
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)...<br>
<br>md grompp is giving error about degrees of freedom. Any advise on this in appreciated...<br><br>Thank you,<br><br>md grompp****************************************************************************<br>aking dummy/rest group for Acceleration containing 2896 elements<br>
Making dummy/rest group for Freeze containing 2896 elements<br>Making dummy/rest group for Energy Mon. containing 2896 elements<br>Making dummy/rest group for VCM containing 2896 elements<br>Number of degrees of freedom in T-Coupling group Eth is 5373.22<br>
Number of degrees of freedom in T-Coupling group EthB is 211.89<br>Number of degrees of freedom in T-Coupling group EthE is 211.89<br>Making dummy/rest group for User1 containing 2896 elements<br>Making dummy/rest group for User2 containing 2896 elements<br>
Making dummy/rest group for XTC containing 2896 elements<br>Making dummy/rest group for Or. Res. Fit containing 2896 elements<br>Making dummy/rest group for QMMM containing 2896 elements<br>T-Coupling has 3 element(s): Eth EthB EthE<br>
Energy Mon. has 1 element(s): rest<br>Acceleration has 1 element(s): rest<br>Freeze has 1 element(s): rest<br>User1 has 1 element(s): rest<br>User2 has 1 element(s): rest<br>VCM has 1 element(s): rest<br>
XTC has 1 element(s): rest<br>Or. Res. Fit has 1 element(s): rest<br>QMMM has 1 element(s): rest<br><br>mdpfile**************************************************************************************<br>
<br>title = PE-Hexane<br>;define = -DPOSRES ; tells gromacs to perform position restrained dynamics/include posre.itp into topology used for position restraint<br>pbc = xyz ; use priodic BCs in all directions<br>
<br>; Run control<br>integrator = md ; type of dynamics algorithm. Here md uses a leap-frog algorithm for integrating Newtons's eq of motion<br>dt = 0.002 ; in ps !<br>
nsteps = 5000 ; length of simulation= nsteps*dt<br>nstcomm = 1 ; frequency for center of mass motion removal<br><br>; Output control<br>nstenergy = 100 ; frequency to write energies to energy file. i.e., energies and other statistical data are stored every 10 steps<br>
nstxout = 100 ; frequency to write coordinates/velocity/force to output trajectory file. how often snapshots are collected= nstxout*dt<br>nstvout = 100<br>nstfout = 0<br>
nstlog = 100 ; frequency to write energies to log file<br>nstxtcout = 10 ; frequency to write coordinates to xtc trajectory<br><br>; Neighbor searching<br>
nstlist = 10 ; frequency to update neighbor list. Neighborlist will be updated at least every 10 steps. Manual p80<br>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<br>
<br>; Electrostatics/VdW<br>coulombtype = Shift ; tells gromacs how to model electrostatics. Coulomb/LJ potential is decreased over the whole range and forces decay smoothly to zero betw$<br>
vdw-type = Shift ; rcoulomb-switch/rvw-switch & rcoulomb/rvdw<br>rcoulomb-switch = 0 ; where to start switching the Coulomb potential<br>rvw-switch = 0 ; where to start switching the LJ potential<br>
<br>; Cut-offs<br>rlist = 1.1 ; in nm. Cut-off distance for short-range neighbor list<br>rcoulomb = 1.0 ; distance for coulomb cut-off<br>rvdw = 1.0 ; distance for coulomb cut-off<br>
<br>; Temperature coupling<br>Tcoupl = berendsen<br>tc-grps = Eth EthB EthE ;HEX ; groups to couple to thermostat; Berendsen temperature coupling is on in these groups<br>
tau_t = 0.1 0.1 0.1 ;0.1 ; time constant for T coupling<br>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<br>
<br>; Pressure coupling<br>Pcoupl = berendsen ; Pressure coupling is not on<br>Pcoupltype = isotropic ; means the box expands and contracts in all directions (x,y,z) in order to maintain the proper pressure<br>
tau_p = 0.5 ; time constant for coupling in ps<br>compressibility = 4.5e-5 ; compressibility of solvent used in simulation in 1/bar<br>ref_p = 1.0 ; reference P for coupling in bar<br>
<br>; Velocity generation Generate velocites is on at 300 K. Manual p155<br>gen_vel = yes ; generate velocites according to Maxwell distribution at T: gen_temp with random gen seed gen_seed<br>
gen_temp = 300.0 ; T for Maxwell distribution<br>gen_seed = 173529 ; used to initialize random generator for random velocities<br><br>; Bonds<br>constraints = all-bonds ; sets the LINCS constraint for all bonds<br>
constraint-algorithm = lincs<br><br><br><br><br><br clear="all"><br><br>