Re: [gmx-users] topology file for two molecules
Justin Cheers, I had just posted a more general query prior to you getting back? It is perhaps not as vague. Gavin Justin A. Lemkul wrote: > > > Gavin Melaugh wrote: >> Hi Justin >> >> I Did the following and it worked. You were right about using one atom >> types directive. If you don't mind I have another query. In all my >> topology files to date (one molecule type), I have always listed the >> atomtypes in the [atomtypes] directive, and used the set up in >> [defaults] below. Is this all that is required for the calculation of >> the LJ energies. I have never used a pair list, a pair types directive >> or a nonbond_params directive. From the output I still get LJ energies >> but I am slightly confused by all the different options. >> > > I can't give a better explanation than what is already in the manual, > specifically section 5.3.3 ([nonbond_params] and whether or not you > need it). Whether or not you need [pairs] depends on the underlying > mechanics of the force field you're using. See section 5.3.5. > > -Justin > >> parameter level >> [defaults] >> ; nbfunccomb-rule gen-pairsfudgeLJ fudgeQQ >> 1 3 yes0.5 0.5 >> >> [atomtypes] >> ;type mass charge ptype sigma(nm) >> epsilon(kjmol-1) >>CB 12.011000 0.00 A 0.355000 0.292880 >>CA 12.011000 -0.115000 A 0.355000 0.292880 >>HC 1.008000 0.115000 A 0.242000 0.125520 >>CU 13.019000 0.265000 A 0.35 0.334720 >>NU 14.007000 -0.597000 A 0.325000 0.711280 >>CH 13.019000 0.332000 A 0.385000 0.334720 >>C3 15.035000 0.00 A 0.390500 0.732200 >>CT 12.011000 -0.18 A 0.35 0.276144 >>HH 1.008000 0.06 A 0.25 0.125520 >> >> #include "tertpentane.itp" >> #include "methylcage.itp" >> >> ;System level >> [system] >> ;the name of this system >> cage and pentane >> >> [molecules] >> ; moleculename number >> tertpentane 1 >> methylcage 1 >> >> >> Justin A. Lemkul wrote: >>> >>> Gavin Melaugh wrote: Hi Justin Cheers. I have attached my pentane itp file. The cage itp is formatted the same. In the examples there never seems to be [atom types] included. I have included it. Does it seem O.K? >>> You only need to use an [atomtypes] directive if you're introducing >>> new atom types into the force field. I don't know if it's >>> necessary. I also don't know if these sections can be discontinuous >>> (i.e., one >>> section present in cage.itp, another in tertpentane.itp). Try the >>> approach I sent you and see. If you get fatal errors, then you may >>> have to assemble a single [atomtypes] directive and put it either in >>> the first .itp file you #include, or before any of the #includes in >>> the .top (since #include really just means "cut-and-paste the stuff >>> here," it works the same). >>> >>> -Justin >>> Gavin Justin A. Lemkul wrote: > Gavin Melaugh wrote: >> Hi Mark. >> >> I have looked this up, but I am a little uncertain. Does one of the >> topologies have to be included within the other as an .itp file. >> If so > No. You #include .itp files to simply add molecules within a > .top; it > would be very rare to #include an .itp within an .itp (although it > can > be done). For your case, your .top is simple: > > #include (force field) > > #include "cage.itp" > #include "pentane.itp" > > [ system ] > My system > > [ molecules ] > Cage1 > Pentane 1 > >> do I only define the [defaults directive] in the .top file i.e. I >> take >> it I don't include this directive in the .itp file as well. >> > The [defaults] directive is provided by whatever force field you > #include. If you're using some custom parameters, then it needs > to be > defined once (and only once) at the top of your .top file. > Otherwise, > you'll get fatal errors from grompp. > > -Justin > >> Cheers >> >> Gavin >> >> Mark Abraham wrote: >>> Look up the include file mechanism on the webpage. >>> >>> Mark >>> >>> - Original Message - >>> From: Gavin Melaugh >>> Date: Tuesday, September 28, 2010 19:04 >>> Subject: [gmx-users] topology file for two molecules >>> To: Discussion list for GROMACS users >>> Hi all I want to run a simulation of one tert-pentane molecule inside one organic cage molecule. I have the topology files for both molecules but obviously I only need one .top file as the input for grompp. What is the most convenient way of having both topologies in one f
Re: [gmx-users] topology file for two molecules
Gavin Melaugh wrote: Hi Justin I Did the following and it worked. You were right about using one atom types directive. If you don't mind I have another query. In all my topology files to date (one molecule type), I have always listed the atomtypes in the [atomtypes] directive, and used the set up in [defaults] below. Is this all that is required for the calculation of the LJ energies. I have never used a pair list, a pair types directive or a nonbond_params directive. From the output I still get LJ energies but I am slightly confused by all the different options. I can't give a better explanation than what is already in the manual, specifically section 5.3.3 ([nonbond_params] and whether or not you need it). Whether or not you need [pairs] depends on the underlying mechanics of the force field you're using. See section 5.3.5. -Justin parameter level [defaults] ; nbfunccomb-rule gen-pairsfudgeLJ fudgeQQ 1 3 yes0.5 0.5 [atomtypes] ;type mass charge ptype sigma(nm) epsilon(kjmol-1) CB 12.011000 0.00 A 0.355000 0.292880 CA 12.011000 -0.115000 A 0.355000 0.292880 HC 1.008000 0.115000 A 0.242000 0.125520 CU 13.019000 0.265000 A 0.35 0.334720 NU 14.007000 -0.597000 A 0.325000 0.711280 CH 13.019000 0.332000 A 0.385000 0.334720 C3 15.035000 0.00 A 0.390500 0.732200 CT 12.011000 -0.18 A 0.35 0.276144 HH 1.008000 0.06 A 0.25 0.125520 #include "tertpentane.itp" #include "methylcage.itp" ;System level [system] ;the name of this system cage and pentane [molecules] ; moleculename number tertpentane 1 methylcage 1 Justin A. Lemkul wrote: Gavin Melaugh wrote: Hi Justin Cheers. I have attached my pentane itp file. The cage itp is formatted the same. In the examples there never seems to be [atom types] included. I have included it. Does it seem O.K? You only need to use an [atomtypes] directive if you're introducing new atom types into the force field. I don't know if it's necessary. I also don't know if these sections can be discontinuous (i.e., one section present in cage.itp, another in tertpentane.itp). Try the approach I sent you and see. If you get fatal errors, then you may have to assemble a single [atomtypes] directive and put it either in the first .itp file you #include, or before any of the #includes in the .top (since #include really just means "cut-and-paste the stuff here," it works the same). -Justin Gavin Justin A. Lemkul wrote: Gavin Melaugh wrote: Hi Mark. I have looked this up, but I am a little uncertain. Does one of the topologies have to be included within the other as an .itp file. If so No. You #include .itp files to simply add molecules within a .top; it would be very rare to #include an .itp within an .itp (although it can be done). For your case, your .top is simple: #include (force field) #include "cage.itp" #include "pentane.itp" [ system ] My system [ molecules ] Cage1 Pentane 1 do I only define the [defaults directive] in the .top file i.e. I take it I don't include this directive in the .itp file as well. The [defaults] directive is provided by whatever force field you #include. If you're using some custom parameters, then it needs to be defined once (and only once) at the top of your .top file. Otherwise, you'll get fatal errors from grompp. -Justin Cheers Gavin Mark Abraham wrote: Look up the include file mechanism on the webpage. Mark - Original Message - From: Gavin Melaugh Date: Tuesday, September 28, 2010 19:04 Subject: [gmx-users] topology file for two molecules To: Discussion list for GROMACS users Hi all I want to run a simulation of one tert-pentane molecule inside one organic cage molecule. I have the topology files for both molecules but obviously I only need one .top file as the input for grompp. What is the most convenient way of having both topologies in one file? Many Thanks Gavin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@g
Re: [gmx-users] topology file for two molecules
Hi Justin I Did the following and it worked. You were right about using one atom types directive. If you don't mind I have another query. In all my topology files to date (one molecule type), I have always listed the atomtypes in the [atomtypes] directive, and used the set up in [defaults] below. Is this all that is required for the calculation of the LJ energies. I have never used a pair list, a pair types directive or a nonbond_params directive. From the output I still get LJ energies but I am slightly confused by all the different options. parameter level [defaults] ; nbfunccomb-rule gen-pairsfudgeLJ fudgeQQ 1 3 yes0.5 0.5 [atomtypes] ;type mass charge ptype sigma(nm) epsilon(kjmol-1) CB 12.011000 0.00 A 0.355000 0.292880 CA 12.011000 -0.115000 A 0.355000 0.292880 HC 1.008000 0.115000 A 0.242000 0.125520 CU 13.019000 0.265000 A 0.35 0.334720 NU 14.007000 -0.597000 A 0.325000 0.711280 CH 13.019000 0.332000 A 0.385000 0.334720 C3 15.035000 0.00 A 0.390500 0.732200 CT 12.011000 -0.18 A 0.35 0.276144 HH 1.008000 0.06 A 0.25 0.125520 #include "tertpentane.itp" #include "methylcage.itp" ;System level [system] ;the name of this system cage and pentane [molecules] ; moleculename number tertpentane 1 methylcage 1 Justin A. Lemkul wrote: > > > Gavin Melaugh wrote: >> Hi Justin >> >> Cheers. I have attached my pentane itp file. The cage itp is formatted >> the same. In the examples there never seems to be [atom types] included. >> I have included it. Does it seem O.K? >> > > You only need to use an [atomtypes] directive if you're introducing > new atom types into the force field. I don't know if it's necessary. > I also don't know if these sections can be discontinuous (i.e., one > section present in cage.itp, another in tertpentane.itp). Try the > approach I sent you and see. If you get fatal errors, then you may > have to assemble a single [atomtypes] directive and put it either in > the first .itp file you #include, or before any of the #includes in > the .top (since #include really just means "cut-and-paste the stuff > here," it works the same). > > -Justin > >> Gavin >> >> Justin A. Lemkul wrote: >>> >>> Gavin Melaugh wrote: Hi Mark. I have looked this up, but I am a little uncertain. Does one of the topologies have to be included within the other as an .itp file. If so >>> No. You #include .itp files to simply add molecules within a .top; it >>> would be very rare to #include an .itp within an .itp (although it can >>> be done). For your case, your .top is simple: >>> >>> #include (force field) >>> >>> #include "cage.itp" >>> #include "pentane.itp" >>> >>> [ system ] >>> My system >>> >>> [ molecules ] >>> Cage1 >>> Pentane 1 >>> do I only define the [defaults directive] in the .top file i.e. I take it I don't include this directive in the .itp file as well. >>> The [defaults] directive is provided by whatever force field you >>> #include. If you're using some custom parameters, then it needs to be >>> defined once (and only once) at the top of your .top file. Otherwise, >>> you'll get fatal errors from grompp. >>> >>> -Justin >>> Cheers Gavin Mark Abraham wrote: > Look up the include file mechanism on the webpage. > > Mark > > - Original Message - > From: Gavin Melaugh > Date: Tuesday, September 28, 2010 19:04 > Subject: [gmx-users] topology file for two molecules > To: Discussion list for GROMACS users > >> Hi all >> >> I want to run a simulation of one tert-pentane molecule inside one >> organic cage molecule. I have the topology files for both >> molecules but >> obviously I only need one .top file as the input for grompp. >> What is the >> most convenient way of having both topologies in one file? >> >> Many Thanks >> >> Gavin >> -- >> gmx-users mailing listgmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface
Re: [gmx-users] topology file for two molecules
O.K Cheers Gavin Justin A. Lemkul wrote: > > > Gavin Melaugh wrote: >> Hi Justin >> >> Cheers. I have attached my pentane itp file. The cage itp is formatted >> the same. In the examples there never seems to be [atom types] included. >> I have included it. Does it seem O.K? >> > > You only need to use an [atomtypes] directive if you're introducing > new atom types into the force field. I don't know if it's necessary. > I also don't know if these sections can be discontinuous (i.e., one > section present in cage.itp, another in tertpentane.itp). Try the > approach I sent you and see. If you get fatal errors, then you may > have to assemble a single [atomtypes] directive and put it either in > the first .itp file you #include, or before any of the #includes in > the .top (since #include really just means "cut-and-paste the stuff > here," it works the same). > > -Justin > >> Gavin >> >> Justin A. Lemkul wrote: >>> >>> Gavin Melaugh wrote: Hi Mark. I have looked this up, but I am a little uncertain. Does one of the topologies have to be included within the other as an .itp file. If so >>> No. You #include .itp files to simply add molecules within a .top; it >>> would be very rare to #include an .itp within an .itp (although it can >>> be done). For your case, your .top is simple: >>> >>> #include (force field) >>> >>> #include "cage.itp" >>> #include "pentane.itp" >>> >>> [ system ] >>> My system >>> >>> [ molecules ] >>> Cage1 >>> Pentane 1 >>> do I only define the [defaults directive] in the .top file i.e. I take it I don't include this directive in the .itp file as well. >>> The [defaults] directive is provided by whatever force field you >>> #include. If you're using some custom parameters, then it needs to be >>> defined once (and only once) at the top of your .top file. Otherwise, >>> you'll get fatal errors from grompp. >>> >>> -Justin >>> Cheers Gavin Mark Abraham wrote: > Look up the include file mechanism on the webpage. > > Mark > > - Original Message - > From: Gavin Melaugh > Date: Tuesday, September 28, 2010 19:04 > Subject: [gmx-users] topology file for two molecules > To: Discussion list for GROMACS users > >> Hi all >> >> I want to run a simulation of one tert-pentane molecule inside one >> organic cage molecule. I have the topology files for both >> molecules but >> obviously I only need one .top file as the input for grompp. >> What is the >> most convenient way of having both topologies in one file? >> >> Many Thanks >> >> Gavin >> -- >> gmx-users mailing listgmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] topology file for two molecules
Gavin Melaugh wrote: Hi Justin Cheers. I have attached my pentane itp file. The cage itp is formatted the same. In the examples there never seems to be [atom types] included. I have included it. Does it seem O.K? You only need to use an [atomtypes] directive if you're introducing new atom types into the force field. I don't know if it's necessary. I also don't know if these sections can be discontinuous (i.e., one section present in cage.itp, another in tertpentane.itp). Try the approach I sent you and see. If you get fatal errors, then you may have to assemble a single [atomtypes] directive and put it either in the first .itp file you #include, or before any of the #includes in the .top (since #include really just means "cut-and-paste the stuff here," it works the same). -Justin Gavin Justin A. Lemkul wrote: Gavin Melaugh wrote: Hi Mark. I have looked this up, but I am a little uncertain. Does one of the topologies have to be included within the other as an .itp file. If so No. You #include .itp files to simply add molecules within a .top; it would be very rare to #include an .itp within an .itp (although it can be done). For your case, your .top is simple: #include (force field) #include "cage.itp" #include "pentane.itp" [ system ] My system [ molecules ] Cage1 Pentane 1 do I only define the [defaults directive] in the .top file i.e. I take it I don't include this directive in the .itp file as well. The [defaults] directive is provided by whatever force field you #include. If you're using some custom parameters, then it needs to be defined once (and only once) at the top of your .top file. Otherwise, you'll get fatal errors from grompp. -Justin Cheers Gavin Mark Abraham wrote: Look up the include file mechanism on the webpage. Mark - Original Message - From: Gavin Melaugh Date: Tuesday, September 28, 2010 19:04 Subject: [gmx-users] topology file for two molecules To: Discussion list for GROMACS users Hi all I want to run a simulation of one tert-pentane molecule inside one organic cage molecule. I have the topology files for both molecules but obviously I only need one .top file as the input for grompp. What is the most convenient way of having both topologies in one file? Many Thanks Gavin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] topology file for two molecules
Hi Justin Cheers. I have attached my pentane itp file. The cage itp is formatted the same. In the examples there never seems to be [atom types] included. I have included it. Does it seem O.K? Gavin Justin A. Lemkul wrote: > > > Gavin Melaugh wrote: >> Hi Mark. >> >> I have looked this up, but I am a little uncertain. Does one of the >> topologies have to be included within the other as an .itp file. If so > > No. You #include .itp files to simply add molecules within a .top; it > would be very rare to #include an .itp within an .itp (although it can > be done). For your case, your .top is simple: > > #include (force field) > > #include "cage.itp" > #include "pentane.itp" > > [ system ] > My system > > [ molecules ] > Cage1 > Pentane 1 > >> do I only define the [defaults directive] in the .top file i.e. I take >> it I don't include this directive in the .itp file as well. >> > > The [defaults] directive is provided by whatever force field you > #include. If you're using some custom parameters, then it needs to be > defined once (and only once) at the top of your .top file. Otherwise, > you'll get fatal errors from grompp. > > -Justin > >> Cheers >> >> Gavin >> >> Mark Abraham wrote: >>> Look up the include file mechanism on the webpage. >>> >>> Mark >>> >>> - Original Message - >>> From: Gavin Melaugh >>> Date: Tuesday, September 28, 2010 19:04 >>> Subject: [gmx-users] topology file for two molecules >>> To: Discussion list for GROMACS users >>> Hi all I want to run a simulation of one tert-pentane molecule inside one organic cage molecule. I have the topology files for both molecules but obviously I only need one .top file as the input for grompp. What is the most convenient way of having both topologies in one file? Many Thanks Gavin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > [atomtypes] ;type mass charge ptype sigma(nm) epsilon(kjmol-1) CT 12.011000 -0.18 A 0.35 0.276144 HC 1.008000 0.06 A 0.25 0.125520 ;Molecular level [moleculetype] ; name nrexcl tertpentane 3 [atoms] ; atomnr type resnr residue namecgnr charge mass 1 CT 1PENT CT 1 0. 12.0110 2 CT 1PENT CT 1 -0.1800 12.0110 3 CT 1PENT CT 1 -0.1800 12.0110 4 CT 1PENT CT 1 -0.1800 12.0110 5 CT 1PENT CT 1 -0.1800 12.0110 6 HC 1PENT HC 1 0.0600 1.0080 7 HC 1PENT HC 1 0.0600 1.0080 8 HC 1PENT HC 1 0.0600 1.0080 9 HC 1PENT HC 1 0.0600 1.0080 10 HC 1PENT HC 1 0.0600 1.0080 11 HC 1PENT HC 1 0.0600 1.0080 12 HC 1PENT HC 1 0.0600 1.0080 13 HC 1PENT HC 1 0.0600 1.0080 14 HC 1PENT HC 1 0.0600 1.0080 15 HC 1PENT HC 1 0.0600 1.0080 16 HC 1PENT HC 1 0.0600 1.0080 17 HC 1PENT HC 1 0.0600 1.0080 [bonds] ; aiaj func b0(nm) kb(kjmol-1 nm-2) 1 2 1 0.1529 224262.4 1 3 1 0.1529 224262.4 1 4 1 0.1529 224262.4 1 5 1 0.1529 224262.4 2 6 1 0.1090 284512.0 2 7 1 0.1090 284512.0 2 8 1 0.1090 284512.0 3 9 1 0.1090 284512.0 310 1 0.1090 284512.0 311 1 0.1090 284512.0 412 1 0.1090 284512.0 413 1 0.1090 284512.0 414 1 0.1090 284512.0 515 1 0.1090 284512.0 516 1 0.1090 284512.0 517 1 0.1090 284512.0 [angles] ; aiajak func theta(deg)ktheta(kjmol-1 rad-2) 2 1 3 1 112.70 488.2728 2 1 4 1 112.70 488.2728 2 1 5 1 112.70 488.2728 3 1 4 1 112.70 488.2728 3 1 5 1 112.70 488.2728 4 1 5 1 112.70 488.2728 1 2 6 1
Re: [gmx-users] topology file for two molecules
Gavin Melaugh wrote: Hi Mark. I have looked this up, but I am a little uncertain. Does one of the topologies have to be included within the other as an .itp file. If so No. You #include .itp files to simply add molecules within a .top; it would be very rare to #include an .itp within an .itp (although it can be done). For your case, your .top is simple: #include (force field) #include "cage.itp" #include "pentane.itp" [ system ] My system [ molecules ] Cage1 Pentane 1 do I only define the [defaults directive] in the .top file i.e. I take it I don't include this directive in the .itp file as well. The [defaults] directive is provided by whatever force field you #include. If you're using some custom parameters, then it needs to be defined once (and only once) at the top of your .top file. Otherwise, you'll get fatal errors from grompp. -Justin Cheers Gavin Mark Abraham wrote: Look up the include file mechanism on the webpage. Mark - Original Message - From: Gavin Melaugh Date: Tuesday, September 28, 2010 19:04 Subject: [gmx-users] topology file for two molecules To: Discussion list for GROMACS users Hi all I want to run a simulation of one tert-pentane molecule inside one organic cage molecule. I have the topology files for both molecules but obviously I only need one .top file as the input for grompp. What is the most convenient way of having both topologies in one file? Many Thanks Gavin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] topology file for two molecules
Hi Mark. I have looked this up, but I am a little uncertain. Does one of the topologies have to be included within the other as an .itp file. If so do I only define the [defaults directive] in the .top file i.e. I take it I don't include this directive in the .itp file as well. Cheers Gavin Mark Abraham wrote: > Look up the include file mechanism on the webpage. > > Mark > > - Original Message - > From: Gavin Melaugh > Date: Tuesday, September 28, 2010 19:04 > Subject: [gmx-users] topology file for two molecules > To: Discussion list for GROMACS users > > > Hi all > > > > I want to run a simulation of one tert-pentane molecule inside one > > organic cage molecule. I have the topology files for both > > molecules but > > obviously I only need one .top file as the input for grompp. > > What is the > > most convenient way of having both topologies in one file? > > > > Many Thanks > > > > Gavin > > -- > > gmx-users mailing listgmx-users@gromacs.org > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to gmx-users-requ...@gromacs.org. > > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] topology file for two molecules
Look up the include file mechanism on the webpage. Mark - Original Message - From: Gavin Melaugh Date: Tuesday, September 28, 2010 19:04 Subject: [gmx-users] topology file for two molecules To: Discussion list for GROMACS users > Hi all > > I want to run a simulation of one tert-pentane molecule inside one > organic cage molecule. I have the topology files for both > molecules but > obviously I only need one .top file as the input for grompp. > What is the > most convenient way of having both topologies in one file? > > Many Thanks > > Gavin > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
