Thanks for providing a small fraction of the information for which Justin asked. You stand a much better chance of ever getting an answer from volunteers if you provide more detail than you think could ever be relevant. :-)
Mark On Wed, Jun 4, 2014 at 7:39 PM, Ali Alizadeh <ali.alizadehmoja...@gmail.com> wrote: > 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. > -- 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.