Dear gromacs users, I am having some difficulty in setting up an NPT simulation, following are the issues
1. With Parinello-Rahman coupling, I am getting the error: Fatal error: The X-size of the box (4.224258) times the triclinic skew factor (1.000000) is smaller than the number of DD cells (5) times the smallest allowed cell size (0.844801) As mentioned in the archives, initially I thought my system is too small to split between different processors. When I load the trajectory I can see that the box is shrinking very fast in the x direction. I have performed the same run with Berendsen thermostat and it ran fine. So changing the pcoupling method can cause such a change? With the berendsen p coupling I have done a benchmark for the system and I am using the optimum number of processors. Will the change in pcoupling affects benchmark as well? some parameters in .mdp file: integrator = sd pbc = xyz rlist = 1.2 coulombtype = PME fourierspacing = 0.12 pme_order = 4 ewald_rtol = 1e-05 optimize_fft = no epsilon_surface = 0 ewald_geometry = 3d rcoulomb = 1.2 vdwtype = Shift rvdw_switch = 0.9 rvdw = 1.0 epsilon_r = 1 DispCorr = EnerPres tc-grps = system tau_t = 2.0 ref_t = 310 pcoupl = Parrinello-Rahman pcoupltype = anisotropic nstpcouple = -1 tau_p = 1.0 2. I changed some of the above mentioned parameters, for example vdwtype to cut-off and DispCorr to energy as shown below: rlist = 1.0 rcoulomb = 1.0 vdwtype = Cut-off rvdw = 1.0 epsilon_r = 1 DispCorr = Ener Again I get the same error: Fatal error: The X-size of the box (5.000070) times the triclinic skew factor (1.000000) is smaller than the number of DD cells (5) times the smallest allowed cell size (1.000000) Also I thought for obtaining more accurate trajectory, I should apply dispersion corrections for both pressure and energy, is this true? 3. In the mailing list I found that tau_p has to be greater than tau_t to avoid larger fluctuations and so changed the parameters as shown below, everything remains same as in question2 except the following: tau_t = 2.0 ref_t = 310 tau_p = 3.0 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. Any help will be appreciated, thanks -- Shyno Mathew PhD student Department of Chemical Engineering Columbia University
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