Hi There,<br>I was trying to run a free energy tutorial given at "<b><i><a href="http://www.dillgroup.ucsf.edu/group/wiki/index.php?title=Free_Energy:_Tutorial">http://www.dillgroup.ucsf.edu/group/wiki/index.php?title=Free_Energy:_Tutorial</a></i></b>"<br>
While trying the very first run i.e. mdrun using "<b>min_lbfgs0.mdp</b>" I ended up with following error<br>------------------------<br>ERROR: With coulombtype = PME, rcoulomb must be equal to rlist<br>calling cpp...<br>
-------------------------<br><br>which i know is valid while using PME for coulombic calculation, but when i tried making rlist=rcoulomb, I got a warning as<br>--------------------------<br>WARNING 1 [file min_lbfgs0.mdp, line unknown]:<br>
For energy conservation with switch/shift potentials, rlist should be 0.1<br> to 0.3 nm larger than rcoulomb/rvdw.<br>-----------------------------<br><br>following is the content of <b>min_lbfgs0.mdp<br>-------------------------</b><b>min_lbfgs0.mdp---------------------<br>
</b><pre>; RUN CONTROL PARAMETERS =<br>integrator = l-bfgs<br>nsteps = 5000<br>; Output frequency for energies to log file and energy file =<br>nstlog = 1<br>nstenergy = 1<br>
; ENERGY MINIMIZATION OPTIONS =<br>; Force tolerance and initial step-size =<br>emtol = 100<br>emstep = 0.01<br>; Max number of iterations in relax_shells =<br>niter = 20<br>
; Number of correction steps to use for L-BFGS minimization<br>nbfgscorr = 10 <br>; NEIGHBORSEARCHING PARAMETERS =<br>; nblist update frequency =<br>nstlist = 1<br>; ns algorithm (simple or grid) =<br>
ns_type = grid<br>; Periodic boundary conditions: xyz or none =<br>pbc = xyz<br>; nblist cut-off =<br>rlist = 1.0<br>domain-decomposition = no<br>; OPTIONS FOR ELECTROSTATICS AND VDW =<br>
; Method for doing electrostatics =<br>coulombtype = pme<br>;rcoulomb-switch = 0<br>rcoulomb = 0.9<br>; Dielectric constant (DC) for cut-off or DC of reaction field =<br>epsilon-r = 1<br>
; Method for doing Van der Waals =<br>vdw-type = switch<br>; cut-off lengths =<br>rvdw-switch = 0.8<br>rvdw = 0.9<br>; Apply long range dispersion corrections for Energy and Pressure =<br>
DispCorr = EnerPres<br>; Spacing for the PME/PPPM FFT grid =<br>fourierspacing = 0.1<br>; FFT grid size, when a value is 0 fourierspacing will be used =<br>fourier_nx = 0<br>fourier_ny = 0<br>
fourier_nz = 0<br>; EWALD/PME/PPPM parameters =<br>pme_order = 6<br>ewald_rtol = 1e-06<br>epsilon_surface = 0<br>optimize_fft = no<br>; Free energy control stuff<br>
free_energy = yes<br>init_lambda = 0.0<br>delta_lambda = 0<br>sc_alpha =0.5<br>sc-power =1.0<br>sc-sigma = 0.3<br>--------------------------------------<br>
<br>Can anybody suggest whether the mdp file has some error or I can use the one with the warning.<br><br><br>Thanks in advance,<br>Vivek<br></pre><br>