Dear gmx users, I am trying to compress a single polymer chain. grompp is giving the error below:
Program mdrun, VERSION 4.0.7 Source code file: ns.c, line: 2299 Fatal error: One of the box vectors has become shorter than twice the cut-off length or box_yy-|box_zy| or box_zz has become smaller than the cut-off. I dont realize the error exactly...I tried compressing with different ref pressures of 30 10 and 1 bar.. can you please guideme whre the problem lies. Actually later I will have to work with much longer chains so this compressing issue can become even more challanging. I wanted to know how I can decide on P coupling parameters (tau_P, pcoupling type or even coupling algorithm ..) when it comes to compressing different chain lengths and different number of chains in the box... Thank you, 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 = 0.001 ; in ps ! nsteps = 4000000 ; 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 = 0 nstfout = 0 nstlog = 1000 ; frequency to write energies to log file nstxtcout = 0 ; 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 = PME ; tells gromacs how to model electrostatics. Shift: Coulomb/LJ potential is decreased over the whole range and forces decay smoothly to zero between vdw-type = Shift ; rcoulomb-switch/rvw-switch & rcoulomb/rvdw rcoulomb-switch = 0 ; where to start switching the Coulomb potential rvdw-switch = 0.9 ;0 ; where to start switching the LJ potential ; Cut-offs rlist = 1.1 ; in nm. Cut-off distance for short-range neighbor list rcoulomb = 1.1 ;1.0 ; distance for coulomb cut-off rvdw = 1.0 ; distance for coulomb cut-off ; Temperature coupling Tcoupl = v-rescale ;berendsen tc-grps = System ;HEX ; groups to couple to thermostat; Berendsen temperature coupling is on in these groups tau_t = 0.1 ;0.1 ; time constant for T coupling ref_t = 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 = Parrinello-Rahman;berendsen Pcoupltype = semiisotropic ;isotropic ; isotropic: means the box expands and contracts in all directions(x,y,z)in order to maintain the proper pressure;semiisotropic: isotropic in x & y directions tau_p = 1 1 ;0.5 ; time constant for coupling in ps compressibility = 4.5e-5 4.5e-5 ; compressibility of solvent used in simulation in 1/bar ref_p = 1.0 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 = none ;all-bonds ; sets the LINCS constraint for all bonds constraint-algorithm = lincs
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