Dear Gromcas users,<br>I am doing some mutation study, NPT simulations. Initially I was using a generic .mdp file I got from my advisor and I was able to run the systems for ~50ns with out any issues. <br>But then I spend time reading about gromacs and created a .mdp file. However, with my .mdp file the runs are crashing with error:<br>
Fatal error:<br>The X-size of the box (4.500406) times the triclinic skew factor (1.000000) is smaller than the number of DD cells (5) times the smallest allowed cell size (0.900000)<br>I understand I can try particle decomposition for this system, but before I want to make sure there is no error in my .mdp file.<br>
When I load the trajectory in the vmd, I can see the box is getting compressed too much. The contents of the current .mdp file are shown below.<br>This .mdp file varies from my advisor's for few parameters which I have shown at the end.<br clear="all">
<br>contents of my .mdp file:<br>title = Yo<br>cpp = /usr/bin/cpp<br>include =<br>define =<br>integrator = sd<br>tinit = 0.0<br>
dt = 0.002<br>nsteps = 50000000<br>nstxout = 1000000<br>nstvout = 1000000<br>nstfout = 1000000<br>nstlog = 10000<br>
nstenergy = 10000<br>nstxtcout = 10000<br>xtc_precision = 1000<br>xtc_grps =<br>energygrps =<br>nstlist = 10<br>ns_type = grid<br>
pbc = xyz<br>rlist = 0.9<br>domain-decomposition = no<br>coulombtype = PME<br>fourierspacing = 0.12<br>pme_order = 4<br>ewald_rtol = 1e-05<br>
optimize_fft = no<br>epsilon_surface = 0<br>ewald_geometry = 3d<br>rcoulomb = 0.9<br>vdwtype = Cut-off<br>rvdw = 0.9<br>epsilon_r = 1<br>
DispCorr = EnerPres<br>; with sd as integrator tcoupl is ignored<br>tc-grps = system<br>; good choice for zeta is 0.5 1/s<br>tau_t = 2.0<br>ref_t = 310<br>
pcoupl = berendsen<br>pcoupltype = anisotropic<br>nstpcouple = -1<br>tau_p = 1.0<br>compressibility = 4.6e-5 4.6e-5 4.6e-5 0 0 0<br>ref_p = 1.0 1.0 1.0 0.0 0.0 0.0<br>
annealing = no<br>;annealing_npoints = 3<br>;annealing_time = 0<br>gen_vel = no<br>gen_temp = 310<br>gen_seed = 173529<br>constraints = all-bonds<br>
constraint_algorithm = LINCS<br>continuation = no<br>lincs_order = 4<br>lincs_iter = 1<br>lincs_warnangle = 30<br>morse = no<br>disre = no<br>
disre_weighting = equal<br>disre_mixed = no<br>disre_fc = 1000<br>disre_tau = 10<br>nstdisreout = 1000<br><br>Parameters that are different in my advisor's file:<br>
DispCorr = Ener<br>tau_t = 0.20<br>compressibility = 5e-6 5e-6 5e-6 0 0 0<br>gen_vel = yes<br>gen_temp = 1<br>gen_seed = 473529<br>
<br>I thought when using vdw cutoff, it is recommended to use dispersion corrections for both pressure and energy. Also can some explain the reason behind this?<br>For tau_t, I used 2 as it is the recommended value for sd integrator in the manual. Also gen_vel has to be no for sd integrator, correct?<br>
Any help will be appreciated!<br><br>Thanks in advance,<br>Shyno<br>-- <br>Shyno Mathew<br>PhD student<br>Department of Chemical Engineering<br>Columbia University<br><br>