Hello,<br><br>Thank you for suggestions. Yes simulation crashes. I am not able see the whole run (1000ps). For all pressures I tired the final simulation box is 2.2*2.2*2.2 nm but simulation crashes before 1000ps. The longest simulation is for 120 bar (727ps). and I think that is why I am not getting the _after_md.gro file after mdrun in none of the simulations. I wanted to take that convoluted structure and replicate the box..
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<pre class="western" style="text-align: justify;">mdrun -s PE60-P120_md.tpr -o PE60-P120_md.tpr -c PE60-P120_after_md -v >& output.mdrun_md</pre>
As you suggested I do the runs in stepwise manner. I need still a little smaller box size than 2*2*2 but I noticed sth during these simulations. When I view the trajectory in ngmx on the menu bar I can select type of box. When I select triclinic or octahedron the final confromation of the chain is more convoluted and fits completely in the box while in case of rectangular box except for pressure of 120 bar for all other pressures I tried most parts of the chain remain outside of the small box. molecules is more extended...I am wondeirng if positions of atoms are calculated and stored how changing the box type in trajectory viewer can affect the structure?!<br>
***********************************************************************************************mdp file I used:<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 = 500000 ; 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 between <br>vdw-type = Shift ; rcoulomb-switch/rvw-switch & rcoulomb/rvdw<br>
rcoulomb-switch = 0 ; where to start switching the Coulomb potential <br>rvdw-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 = System ;HEX ; groups to couple to thermostat; Berendsen temperature coupling is on in these groups <br>
tau_t = 0.1 ;0.1 ; time constant for T coupling <br>ref_t = 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 = 160.0 ; 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>Thanks<br><br><br><br><br clear="all">