[gmx-users] Eror: No parallel Ewald use PME instead!
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 -- 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.
Re: [gmx-users] Eror: No parallel Ewald use PME instead!
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.alizadehmoja...@gmail.com 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 -- 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.
Re: [gmx-users] Eror: No parallel Ewald use PME instead!
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? - 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.
Re: [gmx-users] Eror: No parallel Ewald use PME instead!
I performed an NVT simulation. On Wed, Jun 4, 2014 at 3:12 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? - 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 -- 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.
Re: [gmx-users] Eror: No parallel Ewald use PME instead!
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.
Re: [gmx-users] Eror: No parallel Ewald use PME instead!
Dear Justin, here is my mdp file: title = Liquid CO2 NVT ; Run parameters integrator = md-vv nsteps = 200 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.
Re: [gmx-users] Eror: No parallel Ewald use PME instead!
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 = 200 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.
