Dear Justin, here is my mdp file:
title = Liquid CO2 NVT ; Run parameters integrator = md-vv nsteps = 2000000 dt = 0.001 emtol = 1.0 emstep = 0.0001 ; Output control nstxout = 1000 nstvout = 1000 nstenergy = 1000 nstlog = 100 ; Bond parameters continuation = no constraint_algorithm = lincs constraints = all-bonds ; Neighborsearching ns_type = grid nstlist = 5 rlist = 1.25 rcoulomb = 1.25 rvdw = 1.25 ; Electrostatics coulombtype = ewald fourierspacing = 0.6 ; Temperature coupling is on tcoupl = nose-hoover tc-grps = system tau_t = 0.1 ref_t = 300 ; Pressure coupling is off pcoupl = no ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr = EnerPres ; Velocity generation gen_vel = yes gen_temp = 300 gen_seed = -1 On 6/4/14, 8:29 AM, Ali Alizadeh wrote: > Dear Mark, > > In my first simulation we had these lines: > > ; Electrostatics > coulombtype = PME ; Particle Mesh Ewald for long-range > electrostatics > pme_order = 4 ; cubic interpolation > fourierspacing = 0.12 ; grid spacing for FFT > > ----------------------- > > ; Electrostatics > coulombtype = ewald ; Particle Mesh Ewald for long-range > electrostatics > fourierspacing = 0.6 ; grid spacing for FFT > > ----------------- > > My system in 2nd case is equilibrated. > For anyone to make sense of what you're doing, you'll need to provide complete .mdp files (those settings are not the only determining factors of the validity of the model physics) and evidence of what you're deciding is equilibrated, stable, etc (i.e. real numbers and output from whatever relevant analysis). -Justin > On Wed, Jun 4, 2014 at 4:35 PM, Mark Abraham <mark.j.abra...@gmail.com> > wrote: > >> >> >> >> On Wed, Jun 4, 2014 at 12:42 PM, Ali Alizadeh < >> ali.alizadehmoja...@gmail.com> wrote: >> >>> Dear Mark, >>> >>> Thank you for your reply. >>> >>> When you do not change any parameters except one thing in mdp file(PME to >>> >>> ewald as the paper said that)and then your system converges, for me it means the problem is related to >>> >>> choosing the right method for calculation of the electrostatic potential energy. What's your point on it? >>> >>> >> My point is that a flawed model physics, or a flawed system preparation, >> can get lucky and run stably, or not. On the information given, there is no >> reason to suppose that changing the kind of reciprocal-space approximation >> is relevant. Last time I heard a report like this, the person had changed >> various nonbonded settings "to make things run faster," and in so doing >> produced a junk model physics. >> >> Mark >> >> >>> ----- >>> >>> Mark wrote: >>> >>> Hi, >>> >>> What makes you think the PME algorithm, rather than your choices of >>> settings for it (and twenty other things), is the problem? >>> >>> Mark >>> >>> >>> On Wed, Jun 4, 2014 at 7:57 AM, Ali Alizadeh <ali.alizadehmojarad at gmail.com < https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users>> >>> wrote: >>> >>>> * Dear All users, >>> * >>>>> * I have encounter this error: >>> *>>* ------------- >>> *>* Fatal error: >>> *>* No parallel Ewald. Use PME instead. >>> *>* -------------- >>> *>>* I used 8 cores and gromacs 4.5.5, for doing my calculations. I should use >>> *>* ewald method because >>> *>>* my system can not converge using PME it heats up my system. Are there any >>> *>* suggestions? >>> *>>>>* -- >>> *>* Sincerely >>> *>>* Ali Alizadeh >>> *>* --* >>> -- Sincerely Ali Alizadeh -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.