Dear gmx users,<br><br>I am trying to compress a single polymer chain. grompp is giving the error below:<br><br>Program mdrun, VERSION 4.0.7<br>Source code file: ns.c, line: 2299<br><br>Fatal error:<br>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.<br>
<br>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. <br><br>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...<br>
<br>Thank you,<br><br clear="all"><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 = 0.001 ; in ps !<br>nsteps = 4000000 ; 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 = 0<br>nstfout = 0<br>nstlog = 1000 ; frequency to write energies to log file<br>nstxtcout = 0 ; 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 = PME ; tells gromacs how to model electrostatics. Shift: 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 = 0.9 ;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 = 1.1 ;1.0 ; distance for coulomb cut-off <br>rvdw = 1.0 ; distance for coulomb cut-off <br>
<br>; Temperature coupling <br>Tcoupl = v-rescale ;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 = Parrinello-Rahman;berendsen<br>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<br>
tau_p = 1 1 ;0.5 ; time constant for coupling in ps <br>compressibility = 4.5e-5 4.5e-5 ; compressibility of solvent used in simulation in 1/bar<br>ref_p = 1.0 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 = none ;all-bonds ; sets the LINCS constraint for all bonds<br>
constraint-algorithm = lincs<br><br>