Re: [gmx-users] Trying to add Buck.ham (SR) while the default nonbond type is LJ (SR)
Dear Mark and Justin, I've switched to function type 1 and the simulation runs. I thought the function type would correspond to the type of the comb-rule and missed the information given in the 5.8.1 section of the manual. Thanks a lot! Andreas Am 12.08.2016 um 14:15 schrieb Justin Lemkul: On 8/12/16 8:11 AM, Andreas Mecklenfeld wrote: Hello Mark, sorry for the confusion I've created. My system refers to a solute in water (which has only LJ-parameters for the oxygen atom). Within the solute, there are two approaches to deal with LJ-interactions: 1) intramolecular interactions (including 1-4 and far-off interactions) 2) intermolecular interactions with the oxygens of ambient water There are certain atom types, which handle points 1) and 2) with different sets of LJ-parameters. Since the water oxygen is not included within the solute topology, the pair potential between the affected solute atomtype and the water-oxygen atomtype therefore has to be intermolecular. My .top file looks like this: # [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ 1 2 yes 0.5 0.8333 [ atomtypes ] ;name bond_type mass charge ptype sigma epsilon Amb o3 o3 0.0 0.0 A 2.95992e-01 8.78640e-01 ; 1.66 0.2100 oa oa 0.0 0.0 A 3.06647e-01 8.80314e-01 ; 1.72 0.2104 od od 0.0 0.0 A 2.95992e-01 8.78640e-01 ; 1.66 0.2100 nd nd 0.0 0.0 A 3.25000e-01 7.11280e-01 ; 1.82 0.1700 nl nl 0.0 0.0 A 3.25000e-01 7.11280e-01 ; 1.82 0.1700 sh sh 0.0 0.0 A 3.56359e-01 1.04600e+00 ; 2.00 0.2500 o3i o3i 0.0 0.0 A 0.331503 0.878640; 1.66 0.2100 oai oai 0.0 0.0 A 0.295778 0.880314; 1.72 0.2104 odi odi 0.0 0.0 A 0.320724 0.878640; 1.66 0.2100 ndi ndi 0.0 0.0 A 0.349232 0.711280; 1.82 0.1700 nli nli 0.0 0.0 A 0.299003 0.711280; 1.82 0.1700 shi shi 0.0 0.0 A 0.334978 1.046000; 2.00 0.2500 c3 c3 0.0 0.0 A 3.39967e-01 4.57730e-01 ; 1.91 0.1094 hc hc 0.0 0.0 A 2.64953e-01 6.56888e-02 ; 1.49 0.0157 cc 0.0 0.0 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 oo 0.0 0.0 A 2.95992e-01 8.78640e-01 ; 1.66 0.2100 nn 0.0 0.0 A 3.25000e-01 7.11280e-01 ; 1.82 0.1700 hn hn 0.0 0.0 A 1.06908e-01 6.56888e-02 ; 0.60 0.0157 cc cc 0.0 0.0 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 cd cd 0.0 0.0 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 h4 h4 0.0 0.0 A 2.51055e-01 6.27600e-02 ; 1.41 0.0150 h5 h5 0.0 0.0 A 2.42146e-01 6.27600e-02 ; 1.36 0.0150 na na 0.0 0.0 A 3.25000e-01 7.11280e-01 ; 1.82 0.1700 h1 h1 0.0 0.0 A 2.47135e-01 6.56888e-02 ; 1.39 0.0157 ss ss 0.0 0.0 A 3.56359e-01 1.04600e+00 ; 2.00 0.2500 ca ca 0.0 0.0 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 ha ha 0.0 0.0 A 2.59964e-01 6.27600e-02 ; 1.46 0.0150 oh oh 0.0 0.0 A 3.06647e-01 8.80314e-01 ; 1.72 0.2104 ho ho 0.0 0.0 A 0.0e+00 0.0e+00 ; 0.00 0. HW_tip4pew 1 1.008 0. A 0.0e+00 0.0e+00 OW_tip4pew 8 16.000. A 3.16435e-01 6.80946e-01 MW 0 0. 0. D 0.0e+00 0.0e+00 [ nonbond_params ] OW_tip4pewo3i2 0.3239690.773503 OW_tip4pewoai2 0.3061070.774239 OW_tip4pewodi2 0.3185790.773503 OW_tip4pewndi2 0.3328340.695948 OW_tip4pewnli2 0.3077190.695948 OW_tip4pewshi2 0.3257060.843961 #include "Asn.itp" #include "tip4pew.itp" [ system ] Asn in tip4pew [ molecules ] ; molecule namenr. Asn1 SOL900 # When I comment out the [ non_bond_params ] section, everything works fine, thus I would locate the error to this point. The error I receive is actually the one from the mail subject: ERROR 1 [file topol.top, line 44]: Trying to add Buck.ham (SR) while the default nonbond type is LJ (SR) followed by repetitions regarding the other lines in the [ non_bond_params ] section. You have
Re: [gmx-users] Trying to add Buck.ham (SR) while the default nonbond type is LJ (SR)
On 8/12/16 8:11 AM, Andreas Mecklenfeld wrote: Hello Mark, sorry for the confusion I've created. My system refers to a solute in water (which has only LJ-parameters for the oxygen atom). Within the solute, there are two approaches to deal with LJ-interactions: 1) intramolecular interactions (including 1-4 and far-off interactions) 2) intermolecular interactions with the oxygens of ambient water There are certain atom types, which handle points 1) and 2) with different sets of LJ-parameters. Since the water oxygen is not included within the solute topology, the pair potential between the affected solute atomtype and the water-oxygen atomtype therefore has to be intermolecular. My .top file looks like this: # [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ 1 2 yes 0.5 0.8333 [ atomtypes ] ;name bond_type mass charge ptype sigma epsilon Amb o3 o3 0.0 0.0 A 2.95992e-01 8.78640e-01 ; 1.66 0.2100 oa oa 0.0 0.0 A 3.06647e-01 8.80314e-01 ; 1.72 0.2104 od od 0.0 0.0 A 2.95992e-01 8.78640e-01 ; 1.66 0.2100 nd nd 0.0 0.0 A 3.25000e-01 7.11280e-01 ; 1.82 0.1700 nl nl 0.0 0.0 A 3.25000e-01 7.11280e-01 ; 1.82 0.1700 sh sh 0.0 0.0 A 3.56359e-01 1.04600e+00 ; 2.00 0.2500 o3i o3i 0.0 0.0 A 0.331503 0.878640; 1.66 0.2100 oai oai 0.0 0.0 A 0.295778 0.880314; 1.72 0.2104 odi odi 0.0 0.0 A 0.320724 0.878640; 1.66 0.2100 ndi ndi 0.0 0.0 A 0.349232 0.711280; 1.82 0.1700 nli nli 0.0 0.0 A 0.299003 0.711280; 1.82 0.1700 shi shi 0.0 0.0 A 0.334978 1.046000; 2.00 0.2500 c3 c3 0.0 0.0 A 3.39967e-01 4.57730e-01 ; 1.91 0.1094 hc hc 0.0 0.0 A 2.64953e-01 6.56888e-02 ; 1.49 0.0157 cc 0.0 0.0 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 oo 0.0 0.0 A 2.95992e-01 8.78640e-01 ; 1.66 0.2100 nn 0.0 0.0 A 3.25000e-01 7.11280e-01 ; 1.82 0.1700 hn hn 0.0 0.0 A 1.06908e-01 6.56888e-02 ; 0.60 0.0157 cc cc 0.0 0.0 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 cd cd 0.0 0.0 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 h4 h4 0.0 0.0 A 2.51055e-01 6.27600e-02 ; 1.41 0.0150 h5 h5 0.0 0.0 A 2.42146e-01 6.27600e-02 ; 1.36 0.0150 na na 0.0 0.0 A 3.25000e-01 7.11280e-01 ; 1.82 0.1700 h1 h1 0.0 0.0 A 2.47135e-01 6.56888e-02 ; 1.39 0.0157 ss ss 0.0 0.0 A 3.56359e-01 1.04600e+00 ; 2.00 0.2500 ca ca 0.0 0.0 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 ha ha 0.0 0.0 A 2.59964e-01 6.27600e-02 ; 1.46 0.0150 oh oh 0.0 0.0 A 3.06647e-01 8.80314e-01 ; 1.72 0.2104 ho ho 0.0 0.0 A 0.0e+00 0.0e+00 ; 0.00 0. HW_tip4pew 1 1.008 0. A 0.0e+00 0.0e+00 OW_tip4pew 8 16.000. A 3.16435e-01 6.80946e-01 MW 0 0. 0. D 0.0e+00 0.0e+00 [ nonbond_params ] OW_tip4pewo3i2 0.3239690.773503 OW_tip4pewoai2 0.3061070.774239 OW_tip4pewodi2 0.3185790.773503 OW_tip4pewndi2 0.3328340.695948 OW_tip4pewnli2 0.3077190.695948 OW_tip4pewshi2 0.3257060.843961 #include "Asn.itp" #include "tip4pew.itp" [ system ] Asn in tip4pew [ molecules ] ; molecule namenr. Asn1 SOL900 # When I comment out the [ non_bond_params ] section, everything works fine, thus I would locate the error to this point. The error I receive is actually the one from the mail subject: ERROR 1 [file topol.top, line 44]: Trying to add Buck.ham (SR) while the default nonbond type is LJ (SR) followed by repetitions regarding the other lines in the [ non_bond_params ] section. You have specified type 2 for the [ nonbond_params ] section, which corresponds to Buckingham. If you want normal LJ, set the type field to 1. -Justin Thanks for your help! Andreas Am 12.08.2016 um 09:49 schrieb Mark Abraham: Hi, On Fri, Aug 12, 2016 at 9:16 AM Andreas Mecklenfeld < a.mecklenf...@tu-braunschweig.de> wrote: Hello Mark, thanks for the
Re: [gmx-users] Trying to add Buck.ham (SR) while the default nonbond type is LJ (SR)
Hello Mark, sorry for the confusion I've created. My system refers to a solute in water (which has only LJ-parameters for the oxygen atom). Within the solute, there are two approaches to deal with LJ-interactions: 1) intramolecular interactions (including 1-4 and far-off interactions) 2) intermolecular interactions with the oxygens of ambient water There are certain atom types, which handle points 1) and 2) with different sets of LJ-parameters. Since the water oxygen is not included within the solute topology, the pair potential between the affected solute atomtype and the water-oxygen atomtype therefore has to be intermolecular. My .top file looks like this: # [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ 1 2 yes 0.5 0.8333 [ atomtypes ] ;name bond_type mass charge ptype sigma epsilon Amb o3 o3 0.0 0.0 A 2.95992e-01 8.78640e-01 ; 1.66 0.2100 oa oa 0.0 0.0 A 3.06647e-01 8.80314e-01 ; 1.72 0.2104 od od 0.0 0.0 A 2.95992e-01 8.78640e-01 ; 1.66 0.2100 nd nd 0.0 0.0 A 3.25000e-01 7.11280e-01 ; 1.82 0.1700 nl nl 0.0 0.0 A 3.25000e-01 7.11280e-01 ; 1.82 0.1700 sh sh 0.0 0.0 A 3.56359e-01 1.04600e+00 ; 2.00 0.2500 o3i o3i 0.0 0.0 A 0.331503 0.878640; 1.66 0.2100 oai oai 0.0 0.0 A 0.295778 0.880314; 1.72 0.2104 odi odi 0.0 0.0 A 0.320724 0.878640; 1.66 0.2100 ndi ndi 0.0 0.0 A 0.349232 0.711280; 1.82 0.1700 nli nli 0.0 0.0 A 0.299003 0.711280; 1.82 0.1700 shi shi 0.0 0.0 A 0.334978 1.046000; 2.00 0.2500 c3 c3 0.0 0.0 A 3.39967e-01 4.57730e-01 ; 1.91 0.1094 hc hc 0.0 0.0 A 2.64953e-01 6.56888e-02 ; 1.49 0.0157 cc 0.0 0.0 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 oo 0.0 0.0 A 2.95992e-01 8.78640e-01 ; 1.66 0.2100 nn 0.0 0.0 A 3.25000e-01 7.11280e-01 ; 1.82 0.1700 hn hn 0.0 0.0 A 1.06908e-01 6.56888e-02 ; 0.60 0.0157 cc cc 0.0 0.0 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 cd cd 0.0 0.0 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 h4 h4 0.0 0.0 A 2.51055e-01 6.27600e-02 ; 1.41 0.0150 h5 h5 0.0 0.0 A 2.42146e-01 6.27600e-02 ; 1.36 0.0150 na na 0.0 0.0 A 3.25000e-01 7.11280e-01 ; 1.82 0.1700 h1 h1 0.0 0.0 A 2.47135e-01 6.56888e-02 ; 1.39 0.0157 ss ss 0.0 0.0 A 3.56359e-01 1.04600e+00 ; 2.00 0.2500 ca ca 0.0 0.0 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 ha ha 0.0 0.0 A 2.59964e-01 6.27600e-02 ; 1.46 0.0150 oh oh 0.0 0.0 A 3.06647e-01 8.80314e-01 ; 1.72 0.2104 ho ho 0.0 0.0 A 0.0e+00 0.0e+00 ; 0.00 0. HW_tip4pew 1 1.008 0. A 0.0e+00 0.0e+00 OW_tip4pew 8 16.000. A 3.16435e-01 6.80946e-01 MW 0 0. 0. D 0.0e+00 0.0e+00 [ nonbond_params ] OW_tip4pewo3i2 0.3239690.773503 OW_tip4pewoai2 0.3061070.774239 OW_tip4pewodi2 0.3185790.773503 OW_tip4pewndi2 0.3328340.695948 OW_tip4pewnli2 0.3077190.695948 OW_tip4pewshi2 0.3257060.843961 #include "Asn.itp" #include "tip4pew.itp" [ system ] Asn in tip4pew [ molecules ] ; molecule namenr. Asn1 SOL900 # When I comment out the [ non_bond_params ] section, everything works fine, thus I would locate the error to this point. The error I receive is actually the one from the mail subject: ERROR 1 [file topol.top, line 44]: Trying to add Buck.ham (SR) while the default nonbond type is LJ (SR) followed by repetitions regarding the other lines in the [ non_bond_params ] section. Thanks for your help! Andreas Am 12.08.2016 um 09:49 schrieb Mark Abraham: Hi, On Fri, Aug 12, 2016 at 9:16 AM Andreas Mecklenfeld < a.mecklenf...@tu-braunschweig.de> wrote: Hello Mark, thanks for the reply. The point is, I don't. Ah, I read your original email more closely now. The use of a subject line that reflected your error message rather than
Re: [gmx-users] Trying to add Buck.ham (SR) while the default nonbond type is LJ (SR)
Hi, On Fri, Aug 12, 2016 at 9:16 AM Andreas Mecklenfeld < a.mecklenf...@tu-braunschweig.de> wrote: > Hello Mark, > > thanks for the reply. The point is, I don't. Ah, I read your original email more closely now. The use of a subject line that reflected your error message rather than your intention confused me. > I found some Lennard-Jones > parametrization in literature that distinguishes between intra- and > intermolecular (oxygen atom of water) interactions. Um, typical water models have no intra-molecular LJ interactions. > My intention was > thus to define the specific eps_ij and sigma_ij for the corresponding > atomtypes, which I thought should be dealt with in the [ nonbond_params > ] section. All parameters are for Lennard-Jones and this is the > potential I want to use. I have no idea why the usage of Buckingham is > assumed. I'm using Gromacs 5.1 btw. > Then somewhere (e.g. [nonbond_params]) you are using a number that is being interpreted as a function type that is Buckingham, which of course makes no sense for a code that assumes each atom type has at most one set of LJ parameters. But we haven't seen your full topology or full error message. Mark > Thanks, > Andreas > > > > Am 11.08.2016 um 17:59 schrieb Mark Abraham: > > Hi, > > > > How do you want your atoms with lj parameters to interact with atoms with > > Buckingham parameters? > > > > Mark > > > > On Fri, 5 Aug 2016 08:53 Andreas Mecklenfeld < > > a.mecklenf...@tu-braunschweig.de> wrote: > > > >> Dear Gromacs-users, > >> > >> I'm trying to modify some intermolecular Lennard-Jones interactions > >> based on the GAFF force field. I've altered the topology file according > to > >> > >> > >> > > >> > >> [ defaults ] > >> ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ > >> 1 2 yes 0.5 0.8333 > >> > >> [ atomtypes ] > >> ... > >> > >> [ nonbond_params ] > >> type1type2sigmaepsilon > >> ... > >> > >> #include ... > >> > >>[ system ] > >> ... > >> > >>[ molecules ] > >> ... > >> > >> > >> > >> > >> > > >> > >> Sigma and epsilon for atoms type1 and type2 are calculated according to > >> the Lorentz-Berthelot combination rule. The error I receive is > >> > >> "Trying to add Buck.ham (SR) while the default nonbond type is LJ (SR)", > >> though I obviously want to use LJ and did not intentionally set any flag > >> for Buckingham. Is there any way to fix this? > >> > >> Cheers, > >> > >> Andreas > >> > >> > >> -- > >> M. Sc. Andreas Mecklenfeld > >> Stipendiat > >> > >> Technische Universität Braunschweig > >> Institut für Thermodynamik > >> Hans-Sommer-Straße 5 > >> 38106 Braunschweig > >> Deutschland / Germany > >> > >> Tel: +49 (0)531 391-2634 > >> Fax: +49 (0)531 391-7814 > >> > >> http://www.ift-bs.de > >> > >> -- > >> 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. > > -- > M. Sc. Andreas Mecklenfeld > Stipendiat > > Technische Universität Braunschweig > Institut für Thermodynamik > Hans-Sommer-Straße 5 > 38106 Braunschweig > Deutschland / Germany > > Tel: +49 (0)531 391-2634 > Fax: +49 (0)531 391-7814 > > http://www.ift-bs.de > > -- > 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] Trying to add Buck.ham (SR) while the default nonbond type is LJ (SR)
Hello Mark, thanks for the reply. The point is, I don't. I found some Lennard-Jones parametrization in literature that distinguishes between intra- and intermolecular (oxygen atom of water) interactions. My intention was thus to define the specific eps_ij and sigma_ij for the corresponding atomtypes, which I thought should be dealt with in the [ nonbond_params ] section. All parameters are for Lennard-Jones and this is the potential I want to use. I have no idea why the usage of Buckingham is assumed. I'm using Gromacs 5.1 btw. Thanks, Andreas Am 11.08.2016 um 17:59 schrieb Mark Abraham: Hi, How do you want your atoms with lj parameters to interact with atoms with Buckingham parameters? Mark On Fri, 5 Aug 2016 08:53 Andreas Mecklenfeld < a.mecklenf...@tu-braunschweig.de> wrote: Dear Gromacs-users, I'm trying to modify some intermolecular Lennard-Jones interactions based on the GAFF force field. I've altered the topology file according to [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ 1 2 yes 0.5 0.8333 [ atomtypes ] ... [ nonbond_params ] type1type2sigmaepsilon ... #include ... [ system ] ... [ molecules ] ... Sigma and epsilon for atoms type1 and type2 are calculated according to the Lorentz-Berthelot combination rule. The error I receive is "Trying to add Buck.ham (SR) while the default nonbond type is LJ (SR)", though I obviously want to use LJ and did not intentionally set any flag for Buckingham. Is there any way to fix this? Cheers, Andreas -- M. Sc. Andreas Mecklenfeld Stipendiat Technische Universität Braunschweig Institut für Thermodynamik Hans-Sommer-Straße 5 38106 Braunschweig Deutschland / Germany Tel: +49 (0)531 391-2634 Fax: +49 (0)531 391-7814 http://www.ift-bs.de -- 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. -- M. Sc. Andreas Mecklenfeld Stipendiat Technische Universität Braunschweig Institut für Thermodynamik Hans-Sommer-Straße 5 38106 Braunschweig Deutschland / Germany Tel: +49 (0)531 391-2634 Fax: +49 (0)531 391-7814 http://www.ift-bs.de -- 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] Trying to add Buck.ham (SR) while the default nonbond type is LJ (SR)
Hi, How do you want your atoms with lj parameters to interact with atoms with Buckingham parameters? Mark On Fri, 5 Aug 2016 08:53 Andreas Mecklenfeld < a.mecklenf...@tu-braunschweig.de> wrote: > Dear Gromacs-users, > > I'm trying to modify some intermolecular Lennard-Jones interactions > based on the GAFF force field. I've altered the topology file according to > > > > > [ defaults ] > ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ > 1 2 yes 0.5 0.8333 > > [ atomtypes ] > ... > > [ nonbond_params ] > type1type2sigmaepsilon > ... > > #include ... > > [ system ] > ... > > [ molecules ] > ... > > > > > > > Sigma and epsilon for atoms type1 and type2 are calculated according to > the Lorentz-Berthelot combination rule. The error I receive is > > "Trying to add Buck.ham (SR) while the default nonbond type is LJ (SR)", > though I obviously want to use LJ and did not intentionally set any flag > for Buckingham. Is there any way to fix this? > > Cheers, > > Andreas > > > -- > M. Sc. Andreas Mecklenfeld > Stipendiat > > Technische Universität Braunschweig > Institut für Thermodynamik > Hans-Sommer-Straße 5 > 38106 Braunschweig > Deutschland / Germany > > Tel: +49 (0)531 391-2634 > Fax: +49 (0)531 391-7814 > > http://www.ift-bs.de > > -- > 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.
[gmx-users] Trying to add Buck.ham (SR) while the default nonbond type is LJ (SR)
Dear Gromacs-users, I'm trying to modify some intermolecular Lennard-Jones interactions based on the GAFF force field. I've altered the topology file according to [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ 1 2 yes 0.5 0.8333 [ atomtypes ] ... [ nonbond_params ] type1type2sigmaepsilon ... #include ... [ system ] ... [ molecules ] ... Sigma and epsilon for atoms type1 and type2 are calculated according to the Lorentz-Berthelot combination rule. The error I receive is "Trying to add Buck.ham (SR) while the default nonbond type is LJ (SR)", though I obviously want to use LJ and did not intentionally set any flag for Buckingham. Is there any way to fix this? Cheers, Andreas -- M. Sc. Andreas Mecklenfeld Stipendiat Technische Universität Braunschweig Institut für Thermodynamik Hans-Sommer-Straße 5 38106 Braunschweig Deutschland / Germany Tel: +49 (0)531 391-2634 Fax: +49 (0)531 391-7814 http://www.ift-bs.de -- 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.
