Re: [gmx-users] Grompp warning about topology constrains
Thanks Justin Kind Regards,Ahmed Mashaly From: Justin Lemkul To: gmx-us...@gromacs.org Sent: Tuesday, January 30, 2018 6:00 PM Subject: Re: [gmx-users] Grompp warning about topology constrains On 1/30/18 5:46 AM, Ahmed Mashaly wrote: > > Thanks Justin ... The topology seems fine to me > > The inputs are in this link incase of the text is messed again > https://drive.google.com/open?id=13DzlUl0rLoJBfr_oPf9tLPknAsRNJpuR > > > > title = NVT > define = -DPOSRES ; > > ; Run parameters > integrator = md > dt = 0.002 > nsteps = 25 > > ; Output control > nstlog = 500 > nstxout = 500 > nstvout = 500 > nstfout = 500 > nstcalcenergy = 10 > nstenergy = 500 > > ; Bond parameters > continuation = no > constraint_algorithm = lincs > constraints = all-bonds > lincs_iter = 2 > lincs_order = 4 > shake-tol = 1e-05 > > ; Neighborsearching > cutoff-scheme = Verlet > ns_type = grid > nstlist = 10 > rlist = 1.0 > rvdw = 1.0 > vdwtype = Cut-off > rcoulomb = 1.0 > > ; Electrostatics > coulombtype = pme > pme_order = 4 > fourierspacing = 0.16 > > ; Temperature coupling > tcoupl = V-rescale > tc_grps = Protein Non-Protein > tau_t = 0.1 0.1 > ref_t = 300 300 > > ; Pressure coupling > pcoupl = no > > ; Periodic boundary conditions > pbc = xyz > > ; Dispersion correction > DispCorr = EnerPres > > ; > gen_vel = yes > gen_temp = 300 > gen_seed = -1 > > > > > > The last lines of toplogy: As I said before, the line numbers here and their contents are irrelevant. The error message and its solution are quite clear. You have at least one angle between some atoms i-j-k, in which the masses of atoms i and k differ by at least a factor of 13. In this instance, you shouldn't be constraining all bonds. Set constraints = h-bonds and move ahead. The only force field that I know of that requires all bonds to be constrained is GROMOS, all others normally only constrain bonds to H. -Justin > 79101 [ moleculetype ] > 79102 ; Name nrexcl > 79103 SOL 3 > 79104 > 79105 [ atoms ] > 79106 ; nr type resnr residue atom cgnr charge mass typeB chargeB massB > 79107 ; residue 1 WAT rtp WAT q 0.0 > 79108 1 OW 1 SOL OW 1 -0.834000 16. ; qtot -0.8340 > 79109 2 HW 1 SOL HW1 2 0.417000 1.0080 ; qtot -0.4170 > 79110 3 HW 1 SOL HW2 3 0.417000 1.0080 ; qtot 0. > 79111 > 79112 #ifdef FLEXIBLE > 79113 > 79114 [ bonds ] > 79115 ; ai aj funct c0 c1 c2 c3 > 79116 2 3 1 0.15136 462750.40 > 79117 1 2 1 0.09572 462750.40 > 79118 1 3 1 0.09572 462750.40 > 79119 > 79120 > 79121 #else > 79122 > 79123 [ settles ] > 79124 ; i funct doh dhh > 79125 1 1 0.09572 0.15136 > 79126 > 79127 #endif > 79128 > 79129 [ exclusions ] > 79130 1 2 3 > 79131 2 1 3 > 79132 3 1 2 > 79133 > 79134 [ system ] > 79135 ; Name > 79136 Generic title > 79137 > 79138 [ molecules ] > 79139 ; Compound #mols > 79140 system1 1 > 79141 system2 1 > 79142 system1 1 > 79143 system2 1 > 79144 system1 1 > 79145 system2 1 > 79146 NA 3 > 79147 SOL 49664 > > > > > > Kind Regards, > Ahmed > > > > > > > From: Justin Lemkul > To: gmx-us...@gromacs.org > Sent: Tuesday, January 30, 2018 2:14 AM > Subject: Re: [gmx-users] Grompp warning about topology constrains > > > > > > On 1/29/18 11:03 AM, Ahmed Mashaly wrote: >> Hi, >> I have set up my parameters with tleap, converted to gromacs with Acpype, >> did the minimization. >> >> >> For NVT, when I use grompp, this warning appears: >> WARNING 1 [file gromacs.top, line 79147]: There are atoms at both ends of >> an angle, connected by constraints and with masses that differ by more than >> a factor of 13. This means that there are likely dynamic modes that are >> only very weakly coupled. To ensure good equipartitioning, you need to >> either not use constraints on all bonds (but, if possible, only on bonds >> involving hydrogens) or use integrator = sd or decrease one or more >> tolerances: verlet-buffer-tolerance <= 0.0001, LINCS iterations >= 2, LINCS >> order >= 4 or SHAKE tolerance <= 1e-05 >> >> But in .top file there in this line (the last one) there is no such a thing. > The error appears at the end of topology parsing, so it reports the last > line as being the source, but that's not correct. It's just a reflection > of the fact that you're doing something unstable somewhere in the topology. > >> It worked when I changed the integrator to sd or when I changed the >> constraints to
Re: [gmx-users] Grompp warning about topology constrains
On 1/30/18 5:46 AM, Ahmed Mashaly wrote: Thanks Justin ... The topology seems fine to me The inputs are in this link incase of the text is messed again https://drive.google.com/open?id=13DzlUl0rLoJBfr_oPf9tLPknAsRNJpuR title = NVT define = -DPOSRES ; ; Run parameters integrator = md dt = 0.002 nsteps = 25 ; Output control nstlog = 500 nstxout = 500 nstvout = 500 nstfout = 500 nstcalcenergy = 10 nstenergy = 500 ; Bond parameters continuation = no constraint_algorithm = lincs constraints = all-bonds lincs_iter = 2 lincs_order = 4 shake-tol = 1e-05 ; Neighborsearching cutoff-scheme = Verlet ns_type = grid nstlist = 10 rlist = 1.0 rvdw = 1.0 vdwtype = Cut-off rcoulomb = 1.0 ; Electrostatics coulombtype = pme pme_order = 4 fourierspacing = 0.16 ; Temperature coupling tcoupl = V-rescale tc_grps = Protein Non-Protein tau_t = 0.1 0.1 ref_t = 300 300 ; Pressure coupling pcoupl = no ; Periodic boundary conditions pbc = xyz ; Dispersion correction DispCorr = EnerPres ; gen_vel = yes gen_temp = 300 gen_seed = -1 The last lines of toplogy: As I said before, the line numbers here and their contents are irrelevant. The error message and its solution are quite clear. You have at least one angle between some atoms i-j-k, in which the masses of atoms i and k differ by at least a factor of 13. In this instance, you shouldn't be constraining all bonds. Set constraints = h-bonds and move ahead. The only force field that I know of that requires all bonds to be constrained is GROMOS, all others normally only constrain bonds to H. -Justin 79101 [ moleculetype ] 79102 ; Name nrexcl 79103 SOL 3 79104 79105 [ atoms ] 79106 ; nr type resnr residue atom cgnr charge mass typeB chargeB massB 79107 ; residue 1 WAT rtp WAT q 0.0 79108 1 OW 1 SOL OW 1 -0.834000 16. ; qtot -0.8340 79109 2 HW 1 SOL HW1 2 0.417000 1.0080 ; qtot -0.4170 79110 3 HW 1 SOL HW2 3 0.417000 1.0080 ; qtot 0. 79111 79112 #ifdef FLEXIBLE 79113 79114 [ bonds ] 79115 ; ai aj funct c0 c1 c2 c3 79116 2 3 1 0.15136 462750.40 79117 1 2 1 0.09572 462750.40 79118 1 3 1 0.09572 462750.40 79119 79120 79121 #else 79122 79123 [ settles ] 79124 ; i funct doh dhh 79125 1 1 0.09572 0.15136 79126 79127 #endif 79128 79129 [ exclusions ] 79130 1 2 3 79131 2 1 3 79132 3 1 2 79133 79134 [ system ] 79135 ; Name 79136 Generic title 79137 79138 [ molecules ] 79139 ; Compound #mols 79140 system1 1 79141 system2 1 79142 system1 1 79143 system2 1 79144 system1 1 79145 system2 1 79146 NA 3 79147 SOL 49664 Kind Regards, Ahmed From: Justin Lemkul To: gmx-us...@gromacs.org Sent: Tuesday, January 30, 2018 2:14 AM Subject: Re: [gmx-users] Grompp warning about topology constrains On 1/29/18 11:03 AM, Ahmed Mashaly wrote: Hi, I have set up my parameters with tleap, converted to gromacs with Acpype, did the minimization. For NVT, when I use grompp, this warning appears: WARNING 1 [file gromacs.top, line 79147]: There are atoms at both ends of an angle, connected by constraints and with masses that differ by more than a factor of 13. This means that there are likely dynamic modes that are only very weakly coupled. To ensure good equipartitioning, you need to either not use constraints on all bonds (but, if possible, only on bonds involving hydrogens) or use integrator = sd or decrease one or more tolerances: verlet-buffer-tolerance <= 0.0001, LINCS iterations >= 2, LINCS order >= 4 or SHAKE tolerance <= 1e-05 But in .top file there in this line (the last one) there is no such a thing. The error appears at the end of topology parsing, so it reports the last line as being the source, but that's not correct. It's just a reflection of the fact that you're doing something unstable somewhere in the topology. It worked when I changed the integrator to sd or when I changed the constraints to only h-bonds and not with LINCS iterations >= 2, LINCS order >= 4 or SHAKE tolerance <= 1e-05 I even deleteddefine = -DPOSRES from the .mdp file and got the same warning Position restraints have nothing to do with bond constraints. The text below is basically unintelligible. Please use proper line wrapping in your email client. -Justin this is my input file:itle = NVT define = -DPOSRES ; Run parametersintegrator = md dt = 0.002nsteps = 25 ; Output controlnstlog = 500 nstxout = 500nstvout = 500 nstfout = 500 nstcalcenergy = 10 nstenergy = 500; Bond parameterscontinuation= no constraint_algorithm= lincs constraints = all-bonds lincs_iter = 2 lincs_order = 4 shake-tol = 1e-05 ; Neighborsearchingcutoff-scheme
Re: [gmx-users] Grompp warning about topology constrains
Thanks Justin ... The topology seems fine to me The inputs are in this link incase of the text is messed again https://drive.google.com/open?id=13DzlUl0rLoJBfr_oPf9tLPknAsRNJpuR title = NVT define = -DPOSRES ; ; Run parameters integrator = md dt = 0.002 nsteps = 25 ; Output control nstlog = 500 nstxout = 500 nstvout = 500 nstfout = 500 nstcalcenergy = 10 nstenergy = 500 ; Bond parameters continuation = no constraint_algorithm = lincs constraints = all-bonds lincs_iter = 2 lincs_order = 4 shake-tol = 1e-05 ; Neighborsearching cutoff-scheme = Verlet ns_type = grid nstlist = 10 rlist = 1.0 rvdw = 1.0 vdwtype = Cut-off rcoulomb = 1.0 ; Electrostatics coulombtype = pme pme_order = 4 fourierspacing = 0.16 ; Temperature coupling tcoupl = V-rescale tc_grps = Protein Non-Protein tau_t = 0.1 0.1 ref_t = 300 300 ; Pressure coupling pcoupl = no ; Periodic boundary conditions pbc = xyz ; Dispersion correction DispCorr = EnerPres ; gen_vel = yes gen_temp = 300 gen_seed = -1 The last lines of toplogy: 79101 [ moleculetype ] 79102 ; Name nrexcl 79103 SOL 3 79104 79105 [ atoms ] 79106 ; nr type resnr residue atom cgnr charge mass typeB chargeB massB 79107 ; residue 1 WAT rtp WAT q 0.0 79108 1 OW 1 SOL OW 1 -0.834000 16. ; qtot -0.8340 79109 2 HW 1 SOL HW1 2 0.417000 1.0080 ; qtot -0.4170 79110 3 HW 1 SOL HW2 3 0.417000 1.0080 ; qtot 0. 79111 79112 #ifdef FLEXIBLE 79113 79114 [ bonds ] 79115 ; ai aj funct c0 c1 c2 c3 79116 2 3 1 0.15136 462750.40 79117 1 2 1 0.09572 462750.40 79118 1 3 1 0.09572 462750.40 79119 79120 79121 #else 79122 79123 [ settles ] 79124 ; i funct doh dhh 79125 1 1 0.09572 0.15136 79126 79127 #endif 79128 79129 [ exclusions ] 79130 1 2 3 79131 2 1 3 79132 3 1 2 79133 79134 [ system ] 79135 ; Name 79136 Generic title 79137 79138 [ molecules ] 79139 ; Compound #mols 79140 system1 1 79141 system2 1 79142 system1 1 79143 system2 1 79144 system1 1 79145 system2 1 79146 NA 3 79147 SOL 49664 Kind Regards, Ahmed From: Justin Lemkul To: gmx-us...@gromacs.org Sent: Tuesday, January 30, 2018 2:14 AM Subject: Re: [gmx-users] Grompp warning about topology constrains On 1/29/18 11:03 AM, Ahmed Mashaly wrote: > Hi, > I have set up my parameters with tleap, converted to gromacs with Acpype, did > the minimization. > > > For NVT, when I use grompp, this warning appears: > WARNING 1 [file gromacs.top, line 79147]: There are atoms at both ends of an > angle, connected by constraints and with masses that differ by more than a > factor of 13. This means that there are likely dynamic modes that are only > very weakly coupled. To ensure good equipartitioning, you need to either not > use constraints on all bonds (but, if possible, only on bonds involving > hydrogens) or use integrator = sd or decrease one or more tolerances: > verlet-buffer-tolerance <= 0.0001, LINCS iterations >= 2, LINCS order >= 4 > or SHAKE tolerance <= 1e-05 > > But in .top file there in this line (the last one) there is no such a thing. The error appears at the end of topology parsing, so it reports the last line as being the source, but that's not correct. It's just a reflection of the fact that you're doing something unstable somewhere in the topology. > It worked when I changed the integrator to sd or when I changed the > constraints to only h-bonds and not with LINCS iterations >= 2, LINCS order > >= 4 or SHAKE tolerance <= 1e-05 > > > I even deleteddefine = -DPOSRES > from the .mdp file and got the same warning Position restraints have nothing to do with bond constraints. The text below is basically unintelligible. Please use proper line wrapping in your email client. -Justin > > this is my input file:itle = NVT define = > -DPOSRES ; Run parametersintegrator = md dt > = 0.002nsteps = 25 ; Output controlnstlog > = 500 nstxout = 500nstvout >= 500 nstfout = 500 nstcalcenergy = 10 > nstenergy = 500; Bond parameterscontinuation= > no constraint_algorithm= lincs constraints = > all-bonds lincs_iter = 2 lincs_order = > 4 shake-tol = 1e-05 ; Neighborsearchingcutoff-scheme = > Verletns_type = grid nstlist = 10 > rlist = 1.0rvdw= > 1.0vdwtype = Cut-offrcoulomb= 1.0 >; Electrostaticscoulombtype = pme pme_order = 4
Re: [gmx-users] Grompp warning about topology constrains
On 1/29/18 11:03 AM, Ahmed Mashaly wrote: Hi, I have set up my parameters with tleap, converted to gromacs with Acpype, did the minimization. For NVT, when I use grompp, this warning appears: WARNING 1 [file gromacs.top, line 79147]: There are atoms at both ends of an angle, connected by constraints and with masses that differ by more than a factor of 13. This means that there are likely dynamic modes that are only very weakly coupled. To ensure good equipartitioning, you need to either not use constraints on all bonds (but, if possible, only on bonds involving hydrogens) or use integrator = sd or decrease one or more tolerances: verlet-buffer-tolerance <= 0.0001, LINCS iterations >= 2, LINCS order >= 4 or SHAKE tolerance <= 1e-05 But in .top file there in this line (the last one) there is no such a thing. The error appears at the end of topology parsing, so it reports the last line as being the source, but that's not correct. It's just a reflection of the fact that you're doing something unstable somewhere in the topology. It worked when I changed the integrator to sd or when I changed the constraints to only h-bonds and not with LINCS iterations >= 2, LINCS order >= 4 or SHAKE tolerance <= 1e-05 I even deleteddefine = -DPOSRES from the .mdp file and got the same warning Position restraints have nothing to do with bond constraints. The text below is basically unintelligible. Please use proper line wrapping in your email client. -Justin this is my input file:itle = NVT define = -DPOSRES ; Run parametersintegrator = md dt = 0.002 nsteps = 25 ; Output controlnstlog = 500 nstxout = 500 nstvout = 500 nstfout = 500 nstcalcenergy = 10 nstenergy = 500 ; Bond parameterscontinuation = no constraint_algorithm = lincs constraints = all-bonds lincs_iter = 2 lincs_order = 4 shake-tol = 1e-05 ; Neighborsearchingcutoff-scheme = Verletns_type = grid nstlist = 10 rlist = 1.0 rvdw = 1.0 vdwtype = Cut-offrcoulomb = 1.0 ; Electrostaticscoulombtype = pme pme_order = 4 fourierspacing = 0.16 ; Temperature couplingtcoupl = V-rescaletc_grps = Protein Non-Protein tau_t = 0.1 0.1ref_t = 300 300 ; Pressure couplingpcoupl = no ; Periodic boundary conditionspbc = xyz ; Dispersion correctionDispCorr = EnerPres ;gen_vel = yes gen_temp = 300 gen_seed = -1 And these are the last lines of .top with line numbers (starting 79101) 79101 [ moleculetype ] 79102 ; Name nrexcl 79103 SOL 3 79104 79105 [ atoms ] 79106 ; nr type resnr residue atom cgnr charge mass typeB chargeB massB 79107 ; residue 1 WAT rtp WAT q 0.0 79108 1 OW 1 SOL OW 1 -0.834000 16. ; qtot -0.8340 79109 2 HW 1 SOL HW1 2 0.417000 1.0080 ; qtot -0.4170 79110 3 HW 1 SOL HW2 3 0.417000 1.0080 ; qtot 0. 79111 79112 #ifdef FLEXIBLE 79113 79114 [ bonds ] 79115 ; ai aj funct c0 c1 c2 c3 79116 2 3 1 0.15136 462750.40 79117 1 2 1 0.09572 462750.40 79118 1 3 1 0.09572 462750.40 79119 79120 79121 #else 79122 79123 [ settles ] 79124 ; i funct doh dhh 79125 1 1 0.09572 0.15136 79126 79127 #endif 79128 79129 [ exclusions ] 79130 1 2 3 79131 2 1 3 79132 3 1 2 79133 79134 [ system ] 79135 ; Name 79136 Generic title 79137 79138 [ molecules ] 79139 ; Compound #mols 79140 system1 1 79141 system2 1 79142 system1 1 79143 system2 1 79144 system1 1 79145 system2 1 79146 NA 3 79147 SOL 49664 Thanks,Ahmed -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lis
[gmx-users] Grompp warning about topology constrains
Hi, I have set up my parameters with tleap, converted to gromacs with Acpype, did the minimization. For NVT, when I use grompp, this warning appears: WARNING 1 [file gromacs.top, line 79147]: There are atoms at both ends of an angle, connected by constraints and with masses that differ by more than a factor of 13. This means that there are likely dynamic modes that are only very weakly coupled. To ensure good equipartitioning, you need to either not use constraints on all bonds (but, if possible, only on bonds involving hydrogens) or use integrator = sd or decrease one or more tolerances: verlet-buffer-tolerance <= 0.0001, LINCS iterations >= 2, LINCS order >= 4 or SHAKE tolerance <= 1e-05 But in .top file there in this line (the last one) there is no such a thing. It worked when I changed the integrator to sd or when I changed the constraints to only h-bonds and not with LINCS iterations >= 2, LINCS order >= 4 or SHAKE tolerance <= 1e-05 I even deleteddefine = -DPOSRES from the .mdp file and got the same warning this is my input file:itle = NVT define = -DPOSRES ; Run parametersintegrator = md dt = 0.002 nsteps = 25 ; Output controlnstlog = 500 nstxout = 500 nstvout = 500 nstfout = 500 nstcalcenergy = 10 nstenergy = 500 ; Bond parameterscontinuation = no constraint_algorithm = lincs constraints = all-bonds lincs_iter = 2 lincs_order = 4 shake-tol = 1e-05 ; Neighborsearchingcutoff-scheme = Verletns_type = grid nstlist = 10 rlist = 1.0 rvdw = 1.0 vdwtype = Cut-offrcoulomb = 1.0 ; Electrostaticscoulombtype = pme pme_order = 4 fourierspacing = 0.16 ; Temperature couplingtcoupl = V-rescaletc_grps = Protein Non-Protein tau_t = 0.1 0.1ref_t = 300 300 ; Pressure couplingpcoupl = no ; Periodic boundary conditionspbc = xyz ; Dispersion correctionDispCorr = EnerPres ;gen_vel = yes gen_temp = 300 gen_seed = -1 And these are the last lines of .top with line numbers (starting 79101) 79101 [ moleculetype ] 79102 ; Name nrexcl 79103 SOL 3 79104 79105 [ atoms ] 79106 ; nr type resnr residue atom cgnr charge mass typeB chargeB massB 79107 ; residue 1 WAT rtp WAT q 0.0 79108 1 OW 1 SOL OW 1 -0.834000 16. ; qtot -0.8340 79109 2 HW 1 SOL HW1 2 0.417000 1.0080 ; qtot -0.4170 79110 3 HW 1 SOL HW2 3 0.417000 1.0080 ; qtot 0. 79111 79112 #ifdef FLEXIBLE 79113 79114 [ bonds ] 79115 ; ai aj funct c0 c1 c2 c3 79116 2 3 1 0.15136 462750.40 79117 1 2 1 0.09572 462750.40 79118 1 3 1 0.09572 462750.40 79119 79120 79121 #else 79122 79123 [ settles ] 79124 ; i funct doh dhh 79125 1 1 0.09572 0.15136 79126 79127 #endif 79128 79129 [ exclusions ] 79130 1 2 3 79131 2 1 3 79132 3 1 2 79133 79134 [ system ] 79135 ; Name 79136 Generic title 79137 79138 [ molecules ] 79139 ; Compound #mols 79140 system1 1 79141 system2 1 79142 system1 1 79143 system2 1 79144 system1 1 79145 system2 1 79146 NA 3 79147 SOL 49664 Thanks,Ahmed -- 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.
[gmx-users] grompp warning
Hello GMX users, I added another ligand as a new residue in the topology database, and then build the topology of the liand with pdb2gmx, everything worked well. But I got this warning from grompp for a nvt equilibration after successful minimizations: There are atoms at both ends of an angle, connected by constraints and with masses that differ by more than a factor of 13. This means that there are likely dynamic modes that are only very weakly coupled. To ensure good equipartitioning, you need to either not use constraints on all bonds (but, if possible, only on bonds involving hydrogens) or use integrator = sd or decrease one or more tolerances: verlet-buffer-tolerance <= 0.0001, LINCS iterations >= 2, LINCS order >= 4 or SHAKE tolerance <= 1e-05 It seems that there might be some problem of the topology file. But I can run grompp without any warning if I change the constraints on all bonds to only bonds involving hydrogens. Then I ran a 500 ps NVT equilibration, I checked the trajectory, I did not found any wired angle. Could some one give me some tips? What is the possible reason that I got the warning? Thanks a lot! PS: to be consistent, I also need to apply constraints on all bonds. All the best, Qinghua -- 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] grompp warning: "Overriding Proper Dih. parameters" with type 9 dih.
Issue #2077 created, thanks! On Tue, Nov 15, 2016 at 11:11 AM, Mark Abraham wrote: > Hi, > > Yes that seems a bit inconsistent. Please file a redmine and include e.g. a > tarball of suitable inputs to reproduce what's going on within grompp. > > Mark > > On Tue, Nov 15, 2016 at 3:01 PM Elton Carvalho wrote: > >> Hi, Mark, >> >> Actually, there seems to be a bug somewhere, because if I defined >> three type 9 dihedrals in a file and then I define the same three type >> 9 dihedrals later on, there should be three warnings: one for each >> multiplicity. there were only two warnings, which means the first one >> somehow is silent. >> >> I just did a quick test and re-enabled the first file. The versions >> #included by forcefield.itp and by the .top file are identical. I get >> two arnings (for multiplicities 2 and 3 like on my first email). If I >> comment out these terms, but keep the first one on the second file, I >> get no warnings by grompp. >> >> This means that grompp reads the three terms from file 1 (hiopefully >> adding them up), then reads a bunch of parameters and then reads the >> first term from file 2, which, according to the documentation (and the >> other warnings) would throw a warning and overwrite the prvious >> term(s). No warning is given and the user cannot be sure whether the >> term was overriden or added up (depending on where the code branches >> between these alternatives). >> >> Could I file a redmine issue regarding that? >> >> >> On Tue, Nov 15, 2016 at 5:02 AM, Mark Abraham >> wrote: >> > Hi, >> > >> > Ok that makes sense. Otherwise it would have seemed like it had to be a >> > code bug. >> > >> > Maybe we could add a warning for including the same file twice? Does >> > anybody do that deliberately E.g with different preprocessor variables >> > defined? >> > >> > Mark >> > >> > On Tue, 15 Nov 2016 00:30 Elton Carvalho wrote: >> > >> >> My apologies, >> >> >> >> After careful inspection, I noticed that I had #included a copy of >> >> this ddt.prm file in charmm36-jun2015.ff/forcefield.itp , so the [ >> >> dihedraltypes ] directive is actually loaded twice, hence the >> >> warnings. Removing the #include from forcefield.itp and keeping it in >> >> the .top file eliminated the warnings and the resulting dynamics seems >> >> sane (read: did not explode). >> >> >> >> Lesson learned: don't change the standard forcefield definition files >> >> when doing preliminary testing. Especially in the end of a 12h layover >> >> between flights. >> >> >> >> Thank you for your attention, >> >> -- >> >> Elton >> >> >> >> On Mon, Nov 14, 2016 at 8:04 PM, Elton Carvalho >> wrote: >> >> > Hello, fellow Gromacs Users, >> >> > >> >> > I'm trying to model P3DDT with CGenFF according to the instructions at >> >> > paramchem.org, running the cgenff_charmm2gmx.py script as provided in >> >> > their website. All this is being done on gromacs 2016. >> >> > >> >> > The script converts the .str file generated by paramchem.org to >> >> > gromacs syntax and units. As a first test, I ran a signle >> >> > dodecylthiophene molecule through the process and obtained apparently >> >> > sane .top and .itp files. The .itp file #includes a .prm file, that >> >> > contains the parameters fitted by the paramchem software. >> >> > >> >> > When running gmx grompp (version 2016), I get these two warnings: >> >> > >> >> > === GROMPP WARNING BEGIN === >> >> > >> >> > WARNING 1 [file ddt.prm, line 17]: >> >> > Overriding Proper Dih. parameters. >> >> > Use dihedraltype 9 to allow several multiplicity terms. Only >> >> consecutive >> >> > lines are combined. Non-consective lines overwrite each other. >> >> > >> >> > old: 0 0.8368 1 0 0.8368 1 >> >> > new: CG2R51 CG2R51CG321CG321 9 0.00 >> >> 1.129680 2 >> >> > >> >> > >> >> > WARNING 2 [file ddt.prm, line 18]: >> >> > Overriding Proper Dih. parameters. >> >> > Use dihedraltype 9 to allow several multiplicity terms. Only >> >> consecutive >> >> > lines are combined. Non-consective lines overwrite each other. >> >> > >> >> > old: 0 1.12968 2 0 1.12968 >> 2 >> >> > new: CG2R51 CG2R51CG321CG321 9 0.00 >> >> 0.00 3 >> >> > >> >> > === GROMPP WARNING END === >> >> > >> >> > But the dihedral mentioned is using dihedraltype 9, in lines 16, 17 >> >> > and 18 of the reffered file, as follows: >> >> > >> >> > === ddt.prm RELEVANT SECTION BEGIN (lines 10-21)=== >> >> > >> >> > [ dihedraltypes ] >> >> > ; ijkl func phi0 kphi >> mult >> >> > CG2R51 CG2R51 CG2R51CG321 9 180.0016.736000 >>2 >> >> >CG321 CG2R51 CG2R51 SG2R50 9 180.0029.288000 >>2 >> >> >CG321 CG2R51 CG2R51HGR51 9 180.00 4.184000 >>2 >> >> > CG2R51 CG2R51CG321CG321 9 0.00 0.836800 >>1 >> >> > CG2R51 C
Re: [gmx-users] grompp warning: "Overriding Proper Dih. parameters" with type 9 dih.
Hi, Yes that seems a bit inconsistent. Please file a redmine and include e.g. a tarball of suitable inputs to reproduce what's going on within grompp. Mark On Tue, Nov 15, 2016 at 3:01 PM Elton Carvalho wrote: > Hi, Mark, > > Actually, there seems to be a bug somewhere, because if I defined > three type 9 dihedrals in a file and then I define the same three type > 9 dihedrals later on, there should be three warnings: one for each > multiplicity. there were only two warnings, which means the first one > somehow is silent. > > I just did a quick test and re-enabled the first file. The versions > #included by forcefield.itp and by the .top file are identical. I get > two arnings (for multiplicities 2 and 3 like on my first email). If I > comment out these terms, but keep the first one on the second file, I > get no warnings by grompp. > > This means that grompp reads the three terms from file 1 (hiopefully > adding them up), then reads a bunch of parameters and then reads the > first term from file 2, which, according to the documentation (and the > other warnings) would throw a warning and overwrite the prvious > term(s). No warning is given and the user cannot be sure whether the > term was overriden or added up (depending on where the code branches > between these alternatives). > > Could I file a redmine issue regarding that? > > > On Tue, Nov 15, 2016 at 5:02 AM, Mark Abraham > wrote: > > Hi, > > > > Ok that makes sense. Otherwise it would have seemed like it had to be a > > code bug. > > > > Maybe we could add a warning for including the same file twice? Does > > anybody do that deliberately E.g with different preprocessor variables > > defined? > > > > Mark > > > > On Tue, 15 Nov 2016 00:30 Elton Carvalho wrote: > > > >> My apologies, > >> > >> After careful inspection, I noticed that I had #included a copy of > >> this ddt.prm file in charmm36-jun2015.ff/forcefield.itp , so the [ > >> dihedraltypes ] directive is actually loaded twice, hence the > >> warnings. Removing the #include from forcefield.itp and keeping it in > >> the .top file eliminated the warnings and the resulting dynamics seems > >> sane (read: did not explode). > >> > >> Lesson learned: don't change the standard forcefield definition files > >> when doing preliminary testing. Especially in the end of a 12h layover > >> between flights. > >> > >> Thank you for your attention, > >> -- > >> Elton > >> > >> On Mon, Nov 14, 2016 at 8:04 PM, Elton Carvalho > wrote: > >> > Hello, fellow Gromacs Users, > >> > > >> > I'm trying to model P3DDT with CGenFF according to the instructions at > >> > paramchem.org, running the cgenff_charmm2gmx.py script as provided in > >> > their website. All this is being done on gromacs 2016. > >> > > >> > The script converts the .str file generated by paramchem.org to > >> > gromacs syntax and units. As a first test, I ran a signle > >> > dodecylthiophene molecule through the process and obtained apparently > >> > sane .top and .itp files. The .itp file #includes a .prm file, that > >> > contains the parameters fitted by the paramchem software. > >> > > >> > When running gmx grompp (version 2016), I get these two warnings: > >> > > >> > === GROMPP WARNING BEGIN === > >> > > >> > WARNING 1 [file ddt.prm, line 17]: > >> > Overriding Proper Dih. parameters. > >> > Use dihedraltype 9 to allow several multiplicity terms. Only > >> consecutive > >> > lines are combined. Non-consective lines overwrite each other. > >> > > >> > old: 0 0.8368 1 0 0.8368 1 > >> > new: CG2R51 CG2R51CG321CG321 9 0.00 > >> 1.129680 2 > >> > > >> > > >> > WARNING 2 [file ddt.prm, line 18]: > >> > Overriding Proper Dih. parameters. > >> > Use dihedraltype 9 to allow several multiplicity terms. Only > >> consecutive > >> > lines are combined. Non-consective lines overwrite each other. > >> > > >> > old: 0 1.12968 2 0 1.12968 > 2 > >> > new: CG2R51 CG2R51CG321CG321 9 0.00 > >> 0.00 3 > >> > > >> > === GROMPP WARNING END === > >> > > >> > But the dihedral mentioned is using dihedraltype 9, in lines 16, 17 > >> > and 18 of the reffered file, as follows: > >> > > >> > === ddt.prm RELEVANT SECTION BEGIN (lines 10-21)=== > >> > > >> > [ dihedraltypes ] > >> > ; ijkl func phi0 kphi > mult > >> > CG2R51 CG2R51 CG2R51CG321 9 180.0016.736000 >2 > >> >CG321 CG2R51 CG2R51 SG2R50 9 180.0029.288000 >2 > >> >CG321 CG2R51 CG2R51HGR51 9 180.00 4.184000 >2 > >> > CG2R51 CG2R51CG321CG321 9 0.00 0.836800 >1 > >> > CG2R51 CG2R51CG321CG321 9 0.00 1.129680 >2 > >> > CG2R51 CG2R51CG321CG321 9 0.00 0.00 >3 > >> > CG2R51CG321CG321CG321 9 0.00 0.16
Re: [gmx-users] grompp warning: "Overriding Proper Dih. parameters" with type 9 dih.
Hi, Mark, Actually, there seems to be a bug somewhere, because if I defined three type 9 dihedrals in a file and then I define the same three type 9 dihedrals later on, there should be three warnings: one for each multiplicity. there were only two warnings, which means the first one somehow is silent. I just did a quick test and re-enabled the first file. The versions #included by forcefield.itp and by the .top file are identical. I get two arnings (for multiplicities 2 and 3 like on my first email). If I comment out these terms, but keep the first one on the second file, I get no warnings by grompp. This means that grompp reads the three terms from file 1 (hiopefully adding them up), then reads a bunch of parameters and then reads the first term from file 2, which, according to the documentation (and the other warnings) would throw a warning and overwrite the prvious term(s). No warning is given and the user cannot be sure whether the term was overriden or added up (depending on where the code branches between these alternatives). Could I file a redmine issue regarding that? On Tue, Nov 15, 2016 at 5:02 AM, Mark Abraham wrote: > Hi, > > Ok that makes sense. Otherwise it would have seemed like it had to be a > code bug. > > Maybe we could add a warning for including the same file twice? Does > anybody do that deliberately E.g with different preprocessor variables > defined? > > Mark > > On Tue, 15 Nov 2016 00:30 Elton Carvalho wrote: > >> My apologies, >> >> After careful inspection, I noticed that I had #included a copy of >> this ddt.prm file in charmm36-jun2015.ff/forcefield.itp , so the [ >> dihedraltypes ] directive is actually loaded twice, hence the >> warnings. Removing the #include from forcefield.itp and keeping it in >> the .top file eliminated the warnings and the resulting dynamics seems >> sane (read: did not explode). >> >> Lesson learned: don't change the standard forcefield definition files >> when doing preliminary testing. Especially in the end of a 12h layover >> between flights. >> >> Thank you for your attention, >> -- >> Elton >> >> On Mon, Nov 14, 2016 at 8:04 PM, Elton Carvalho wrote: >> > Hello, fellow Gromacs Users, >> > >> > I'm trying to model P3DDT with CGenFF according to the instructions at >> > paramchem.org, running the cgenff_charmm2gmx.py script as provided in >> > their website. All this is being done on gromacs 2016. >> > >> > The script converts the .str file generated by paramchem.org to >> > gromacs syntax and units. As a first test, I ran a signle >> > dodecylthiophene molecule through the process and obtained apparently >> > sane .top and .itp files. The .itp file #includes a .prm file, that >> > contains the parameters fitted by the paramchem software. >> > >> > When running gmx grompp (version 2016), I get these two warnings: >> > >> > === GROMPP WARNING BEGIN === >> > >> > WARNING 1 [file ddt.prm, line 17]: >> > Overriding Proper Dih. parameters. >> > Use dihedraltype 9 to allow several multiplicity terms. Only >> consecutive >> > lines are combined. Non-consective lines overwrite each other. >> > >> > old: 0 0.8368 1 0 0.8368 1 >> > new: CG2R51 CG2R51CG321CG321 9 0.00 >> 1.129680 2 >> > >> > >> > WARNING 2 [file ddt.prm, line 18]: >> > Overriding Proper Dih. parameters. >> > Use dihedraltype 9 to allow several multiplicity terms. Only >> consecutive >> > lines are combined. Non-consective lines overwrite each other. >> > >> > old: 0 1.12968 2 0 1.12968 2 >> > new: CG2R51 CG2R51CG321CG321 9 0.00 >> 0.00 3 >> > >> > === GROMPP WARNING END === >> > >> > But the dihedral mentioned is using dihedraltype 9, in lines 16, 17 >> > and 18 of the reffered file, as follows: >> > >> > === ddt.prm RELEVANT SECTION BEGIN (lines 10-21)=== >> > >> > [ dihedraltypes ] >> > ; ijkl func phi0 kphi mult >> > CG2R51 CG2R51 CG2R51CG321 9 180.0016.736000 2 >> >CG321 CG2R51 CG2R51 SG2R50 9 180.0029.288000 2 >> >CG321 CG2R51 CG2R51HGR51 9 180.00 4.184000 2 >> > CG2R51 CG2R51CG321CG321 9 0.00 0.836800 1 >> > CG2R51 CG2R51CG321CG321 9 0.00 1.129680 2 >> > CG2R51 CG2R51CG321CG321 9 0.00 0.00 3 >> > CG2R51CG321CG321CG321 9 0.00 0.167360 3 >> > CG2R51CG321CG321 HGA2 9 0.00 0.836800 3 >> > >> > === ddt.prm RELEVANT SECTION END === >> > >> > As you can see, the dihedraltype is 9 and the different multiplicities >> > of the "CG2R51 CG2R51CG321CG321" dihedral are on adjacent >> > lines (16, 17 and 18 of the original file. Note that the first warning >> > is about overriding the parameters on line 16 with those on line 17, >
Re: [gmx-users] grompp warning: "Overriding Proper Dih. parameters" with type 9 dih.
Hi, Ok that makes sense. Otherwise it would have seemed like it had to be a code bug. Maybe we could add a warning for including the same file twice? Does anybody do that deliberately E.g with different preprocessor variables defined? Mark On Tue, 15 Nov 2016 00:30 Elton Carvalho wrote: > My apologies, > > After careful inspection, I noticed that I had #included a copy of > this ddt.prm file in charmm36-jun2015.ff/forcefield.itp , so the [ > dihedraltypes ] directive is actually loaded twice, hence the > warnings. Removing the #include from forcefield.itp and keeping it in > the .top file eliminated the warnings and the resulting dynamics seems > sane (read: did not explode). > > Lesson learned: don't change the standard forcefield definition files > when doing preliminary testing. Especially in the end of a 12h layover > between flights. > > Thank you for your attention, > -- > Elton > > On Mon, Nov 14, 2016 at 8:04 PM, Elton Carvalho wrote: > > Hello, fellow Gromacs Users, > > > > I'm trying to model P3DDT with CGenFF according to the instructions at > > paramchem.org, running the cgenff_charmm2gmx.py script as provided in > > their website. All this is being done on gromacs 2016. > > > > The script converts the .str file generated by paramchem.org to > > gromacs syntax and units. As a first test, I ran a signle > > dodecylthiophene molecule through the process and obtained apparently > > sane .top and .itp files. The .itp file #includes a .prm file, that > > contains the parameters fitted by the paramchem software. > > > > When running gmx grompp (version 2016), I get these two warnings: > > > > === GROMPP WARNING BEGIN === > > > > WARNING 1 [file ddt.prm, line 17]: > > Overriding Proper Dih. parameters. > > Use dihedraltype 9 to allow several multiplicity terms. Only > consecutive > > lines are combined. Non-consective lines overwrite each other. > > > > old: 0 0.8368 1 0 0.8368 1 > > new: CG2R51 CG2R51CG321CG321 9 0.00 > 1.129680 2 > > > > > > WARNING 2 [file ddt.prm, line 18]: > > Overriding Proper Dih. parameters. > > Use dihedraltype 9 to allow several multiplicity terms. Only > consecutive > > lines are combined. Non-consective lines overwrite each other. > > > > old: 0 1.12968 2 0 1.12968 2 > > new: CG2R51 CG2R51CG321CG321 9 0.00 > 0.00 3 > > > > === GROMPP WARNING END === > > > > But the dihedral mentioned is using dihedraltype 9, in lines 16, 17 > > and 18 of the reffered file, as follows: > > > > === ddt.prm RELEVANT SECTION BEGIN (lines 10-21)=== > > > > [ dihedraltypes ] > > ; ijkl func phi0 kphi mult > > CG2R51 CG2R51 CG2R51CG321 9 180.0016.736000 2 > >CG321 CG2R51 CG2R51 SG2R50 9 180.0029.288000 2 > >CG321 CG2R51 CG2R51HGR51 9 180.00 4.184000 2 > > CG2R51 CG2R51CG321CG321 9 0.00 0.836800 1 > > CG2R51 CG2R51CG321CG321 9 0.00 1.129680 2 > > CG2R51 CG2R51CG321CG321 9 0.00 0.00 3 > > CG2R51CG321CG321CG321 9 0.00 0.167360 3 > > CG2R51CG321CG321 HGA2 9 0.00 0.836800 3 > > > > === ddt.prm RELEVANT SECTION END === > > > > As you can see, the dihedraltype is 9 and the different multiplicities > > of the "CG2R51 CG2R51CG321CG321" dihedral are on adjacent > > lines (16, 17 and 18 of the original file. Note that the first warning > > is about overriding the parameters on line 16 with those on line 17, > > so this dihedral is not defined somewhere else). No wildcard dihedral > > parameters are present in the loaded .itp files. > > > > Why does grompp warn me that it's "Overriding Proper Dih. parameters", > > even though the parameters are entered (to the best of my knowledge) > > as instructed both in the warning and in Section 5.3.3 of the > > Reference Manual? How can I check whether it really did override the > > parameter or added the different terms? > > > > Thanks in advance, > > -- > > Elton Carvalho > > > > -- > Elton Carvalho > -- > 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-us
Re: [gmx-users] grompp warning: "Overriding Proper Dih. parameters" with type 9 dih.
My apologies, After careful inspection, I noticed that I had #included a copy of this ddt.prm file in charmm36-jun2015.ff/forcefield.itp , so the [ dihedraltypes ] directive is actually loaded twice, hence the warnings. Removing the #include from forcefield.itp and keeping it in the .top file eliminated the warnings and the resulting dynamics seems sane (read: did not explode). Lesson learned: don't change the standard forcefield definition files when doing preliminary testing. Especially in the end of a 12h layover between flights. Thank you for your attention, -- Elton On Mon, Nov 14, 2016 at 8:04 PM, Elton Carvalho wrote: > Hello, fellow Gromacs Users, > > I'm trying to model P3DDT with CGenFF according to the instructions at > paramchem.org, running the cgenff_charmm2gmx.py script as provided in > their website. All this is being done on gromacs 2016. > > The script converts the .str file generated by paramchem.org to > gromacs syntax and units. As a first test, I ran a signle > dodecylthiophene molecule through the process and obtained apparently > sane .top and .itp files. The .itp file #includes a .prm file, that > contains the parameters fitted by the paramchem software. > > When running gmx grompp (version 2016), I get these two warnings: > > === GROMPP WARNING BEGIN === > > WARNING 1 [file ddt.prm, line 17]: > Overriding Proper Dih. parameters. > Use dihedraltype 9 to allow several multiplicity terms. Only consecutive > lines are combined. Non-consective lines overwrite each other. > > old: 0 0.8368 1 0 0.8368 1 > new: CG2R51 CG2R51CG321CG321 9 0.00 1.129680 2 > > > WARNING 2 [file ddt.prm, line 18]: > Overriding Proper Dih. parameters. > Use dihedraltype 9 to allow several multiplicity terms. Only consecutive > lines are combined. Non-consective lines overwrite each other. > > old: 0 1.12968 2 0 1.12968 2 > new: CG2R51 CG2R51CG321CG321 9 0.00 0.00 3 > > === GROMPP WARNING END === > > But the dihedral mentioned is using dihedraltype 9, in lines 16, 17 > and 18 of the reffered file, as follows: > > === ddt.prm RELEVANT SECTION BEGIN (lines 10-21)=== > > [ dihedraltypes ] > ; ijkl func phi0 kphi mult > CG2R51 CG2R51 CG2R51CG321 9 180.0016.736000 2 >CG321 CG2R51 CG2R51 SG2R50 9 180.0029.288000 2 >CG321 CG2R51 CG2R51HGR51 9 180.00 4.184000 2 > CG2R51 CG2R51CG321CG321 9 0.00 0.836800 1 > CG2R51 CG2R51CG321CG321 9 0.00 1.129680 2 > CG2R51 CG2R51CG321CG321 9 0.00 0.00 3 > CG2R51CG321CG321CG321 9 0.00 0.167360 3 > CG2R51CG321CG321 HGA2 9 0.00 0.836800 3 > > === ddt.prm RELEVANT SECTION END === > > As you can see, the dihedraltype is 9 and the different multiplicities > of the "CG2R51 CG2R51CG321CG321" dihedral are on adjacent > lines (16, 17 and 18 of the original file. Note that the first warning > is about overriding the parameters on line 16 with those on line 17, > so this dihedral is not defined somewhere else). No wildcard dihedral > parameters are present in the loaded .itp files. > > Why does grompp warn me that it's "Overriding Proper Dih. parameters", > even though the parameters are entered (to the best of my knowledge) > as instructed both in the warning and in Section 5.3.3 of the > Reference Manual? How can I check whether it really did override the > parameter or added the different terms? > > Thanks in advance, > -- > Elton Carvalho -- Elton Carvalho -- 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.
[gmx-users] grompp warning: "Overriding Proper Dih. parameters" with type 9 dih.
Hello, fellow Gromacs Users, I'm trying to model P3DDT with CGenFF according to the instructions at paramchem.org, running the cgenff_charmm2gmx.py script as provided in their website. All this is being done on gromacs 2016. The script converts the .str file generated by paramchem.org to gromacs syntax and units. As a first test, I ran a signle dodecylthiophene molecule through the process and obtained apparently sane .top and .itp files. The .itp file #includes a .prm file, that contains the parameters fitted by the paramchem software. When running gmx grompp (version 2016), I get these two warnings: === GROMPP WARNING BEGIN === WARNING 1 [file ddt.prm, line 17]: Overriding Proper Dih. parameters. Use dihedraltype 9 to allow several multiplicity terms. Only consecutive lines are combined. Non-consective lines overwrite each other. old: 0 0.8368 1 0 0.8368 1 new: CG2R51 CG2R51CG321CG321 9 0.00 1.129680 2 WARNING 2 [file ddt.prm, line 18]: Overriding Proper Dih. parameters. Use dihedraltype 9 to allow several multiplicity terms. Only consecutive lines are combined. Non-consective lines overwrite each other. old: 0 1.12968 2 0 1.12968 2 new: CG2R51 CG2R51CG321CG321 9 0.00 0.00 3 === GROMPP WARNING END === But the dihedral mentioned is using dihedraltype 9, in lines 16, 17 and 18 of the reffered file, as follows: === ddt.prm RELEVANT SECTION BEGIN (lines 10-21)=== [ dihedraltypes ] ; ijkl func phi0 kphi mult CG2R51 CG2R51 CG2R51CG321 9 180.0016.736000 2 CG321 CG2R51 CG2R51 SG2R50 9 180.0029.288000 2 CG321 CG2R51 CG2R51HGR51 9 180.00 4.184000 2 CG2R51 CG2R51CG321CG321 9 0.00 0.836800 1 CG2R51 CG2R51CG321CG321 9 0.00 1.129680 2 CG2R51 CG2R51CG321CG321 9 0.00 0.00 3 CG2R51CG321CG321CG321 9 0.00 0.167360 3 CG2R51CG321CG321 HGA2 9 0.00 0.836800 3 === ddt.prm RELEVANT SECTION END === As you can see, the dihedraltype is 9 and the different multiplicities of the "CG2R51 CG2R51CG321CG321" dihedral are on adjacent lines (16, 17 and 18 of the original file. Note that the first warning is about overriding the parameters on line 16 with those on line 17, so this dihedral is not defined somewhere else). No wildcard dihedral parameters are present in the loaded .itp files. Why does grompp warn me that it's "Overriding Proper Dih. parameters", even though the parameters are entered (to the best of my knowledge) as instructed both in the warning and in Section 5.3.3 of the Reference Manual? How can I check whether it really did override the parameter or added the different terms? Thanks in advance, -- Elton Carvalho -- 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.
