Dear gromacs users: How would we be able to construct a force field for an ionic liquid? Is there any methodology or reference that we can study?
Thanks! Andy On 6/30/14, gromacs.org_gmx-users-requ...@maillist.sys.kth.se <gromacs.org_gmx-users-requ...@maillist.sys.kth.se> wrote: > Send gromacs.org_gmx-users mailing list submissions to > gromacs.org_gmx-users@maillist.sys.kth.se > > To subscribe or unsubscribe via the World Wide Web, visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > or, via email, send a message with subject or body 'help' to > gromacs.org_gmx-users-requ...@maillist.sys.kth.se > > You can reach the person managing the list at > gromacs.org_gmx-users-ow...@maillist.sys.kth.se > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of gromacs.org_gmx-users digest..." > > > Today's Topics: > > 1. Re: CNT with BN co doping (Dr. Vitaly Chaban) > 2. Re: How to calculate Box Vectors in the last line of the .gro > file? (Dr. Vitaly Chaban) > 3. Re: Questions regarding converting .GRO files to .TOP files > (Dr. Vitaly Chaban) > 4. Re: CNT with BN co doping (akari karin) > 5. Re: CNT with BN co doping (Dr. Vitaly Chaban) > 6. Re: Questions regarding converting .GRO files to .TOP files > (Justin Lemkul) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 30 Jun 2014 12:01:36 +0200 > From: "Dr. Vitaly Chaban" <vvcha...@gmail.com> > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] CNT with BN co doping > Message-ID: > <capxdd+yn8ixgxygb9vsiwy41uizq5elnw7m58dihviy_lqh...@mail.gmail.com> > Content-Type: text/plain; charset=UTF-8 > > Simulation of doped nanostructures is much more complicated than > described below. You must account for the effect of your new fragments > on electron density of the entire nanostructure. There is enough > evidence that an additive approach fails here. > > Good luck. > > Dr. Vitaly V. Chaban > > > On Mon, Jun 30, 2014 at 11:45 AM, akari karin <j.akarika...@gmail.com> > wrote: >> I am trying to simulate carbon nanotubes with some doping. The way i am >> doping my nanotube is by B-N codoping. >> >> i generated the structure but stuck with the topology. i know i need to >> have the bonded and nonbonded interaction parameters for Boron and >> Nitrogen >> to do the work but i dont understand how i can get those. >> >> i am using the modified oplsaa force field for the simulation of CNT >> structure. will the default parameters in the oplsaa be okay for my >> simulation? if not how can i get the parameters? >> >> thanks in advance >> -- >> 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. > > > ------------------------------ > > Message: 2 > Date: Mon, 30 Jun 2014 12:04:47 +0200 > From: "Dr. Vitaly Chaban" <vvcha...@gmail.com> > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] How to calculate Box Vectors in the last line > of the .gro file? > Message-ID: > <capxdd+a7q0fmn0modnthdjb7pnlajzmggx6s51undpzwwrk...@mail.gmail.com> > Content-Type: text/plain; charset=UTF-8 > > You need to set the box vectors with respect to system density or > anticipated system density. > > > Dr. Vitaly V. Chaban > > > On Sun, Jun 29, 2014 at 9:06 PM, Todor Antonijevic <t_ant...@uncg.edu> > wrote: >> Hi, >> >> I cannot obtain the last line (box vectors *1.82060 1.82060 1.82060*) of >> the .gro file. >> >> *Can anyone explain me how the last line is calculated?* >> >> The example is from the manual: >> >> "MD of 2 waters, t= 0.0 >> >> 6 >> 1WATER OW1 1 0.126 1.624 1.679 0.1227 -0.0580 0.0434 >> 1WATER HW2 2 0.190 1.661 1.747 0.8085 0.3191 -0.7791 >> 1WATER HW3 3 0.177 1.568 1.613 -0.9045 -2.6469 1.3180 >> 2WATER OW1 4 1.275 0.053 0.622 0.2519 0.3140 -0.1734 >> 2WATER HW2 5 1.337 0.002 0.680 -1.0641 -1.1349 0.0257 >> 2WATER HW3 6 1.326 0.120 0.568 1.9427 -0.8216 -0.0244 >> >> *1.82060 1.82060 1.82060*" >> >> Thank you very much >> -- >> 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. > > > ------------------------------ > > Message: 3 > Date: Mon, 30 Jun 2014 12:10:35 +0200 > From: "Dr. Vitaly Chaban" <vvcha...@gmail.com> > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Questions regarding converting .GRO files to > .TOP files > Message-ID: > <capxdd+zugo0lhlnyejd2h1_mbvaxjccbabndnl0egzfcjz2...@mail.gmail.com> > Content-Type: text/plain; charset=UTF-8 > > I believe x2top works nice only when you have a single molecule in a > structure file. > > Perhaps, the algorithm wants to connect molecules, which are not > actually connected, and goes crazy, but it is just a guess. > > > Dr. Vitaly V. Chaban > > > On Mon, Jun 30, 2014 at 5:46 AM, Andy Chao <ac...@energiaq.com> wrote: >> Dear GROMACS users: >> >> I have a few questions about converting the .GRO files to .TOP files. I >> first used Python to create a sheet of graphene layer by using the >> following Python codes: >> >> from ase import * >> from ase.structure import graphene_nanoribbon >> from ase io.import* >> gnr1 = graphene_nanoribbon(8,8, type='armchair') >> write('graphene.pdb', gnr1, format='pdb') >> >> Second, I used the following codes to convert the PDB file to GRO file >> for >> the cathode layer: >> >> editconf -f graphene.pdb -o graphene_cathode.gro >> >> Third, I used the following codes to convert the PDB files to GRO file >> for >> the anode layer: >> >> editconf -f graphene.pdb -translate 0 5.0 -o graphene_anode.gro >> >> Fourth, I combined the cathode layer and the anode layer to one complete >> structure according to the following code: >> >> genbox -cs graphene_cathode.gro -cp graphene_anode.gro -maxsol 5000 -box >> 3 >> 1 3 -o electrodes.gro >> >> Fifth, I converted the electrode gro file to top file according to the >> following code: >> >> g_x2top -f electrodes.gro -ff cnt_oplsaa -o device.top >> >> GROMACS showed that there are carbon atoms force field that can not be >> found in the atomname2type.n2t file. >> >> part of the error message is shown as the following: >> >> Can not find forcefield for atom C-447 with 6 bonds >> Can not find forcefield for atom C-448 with 5 bonds.... >> >> Fatal error: >> >> Could only find a forcefield type for 364 out of 512 atoms. >> >> My atomname2type.n2t file consists of the following: >> >> C opls_145 -0.12 12.011 3 C 0.150 C 0.150 H 0.108 >> C opls_145 -0.12 12.011 3 C 0.133 C 0.150 O 0.140 >> C opls_145 0.0 12.011 3 C 0.140 C 0.140 C 0.140 >> C opls_145 0.0 12.011 2 C 0.140 C 0.140 >> >> However, the TOP files for the cathode layer or the anode layer can be >> converted from the GRO files without any error as the following: >> >> g_x2top -f graphene_cathode.gro -ff cnt_oplsaa -o graphene_cathode.top >> g_x2top -f graphene_anode.gro -ff cnt_oplsaa -o graphene_anode.top >> >> can people explain why? What is the reason behind the error message that >> I >> got when converting the GRO file of two combined layer of graphene to the >> TOP file while the same atomname2type.n2t file is used? >> >> >> Thank you very much! >> >> Andy >> -- >> 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. > > > ------------------------------ > > Message: 4 > Date: Mon, 30 Jun 2014 16:33:41 +0600 > From: akari karin <j.akarika...@gmail.com> > To: gmx-us...@gromacs.org, vvcha...@gmail.com > Subject: Re: [gmx-users] CNT with BN co doping > Message-ID: > <caaiesouvdva6ocfbwidqa8kyf1z7h8nbfjvvbhf0dptuoob...@mail.gmail.com> > Content-Type: text/plain; charset=UTF-8 > > thanks Dr. Vitaly V. Chaban for your reply. > > i already simulated the CNT without doping and i have developed a structure > with the doped CNT. > > now if i add the dopant atoms in my forcefield file (for example, in my > case i add nonbonded parameters to my ffnonbond.itp and bonded parameters > to my bonded.itp and so on) will it be the correct way to do the > simulation? > > and it would be very nice if you could explain the statement, > > "You must account for the effect of your new fragments on electron density > of the entire nanostructure." > > a little bit further. > > thanks for your time > > > > > On Mon, Jun 30, 2014 at 4:01 PM, Dr. Vitaly Chaban <vvcha...@gmail.com> > wrote: > >> Simulation of doped nanostructures is much more complicated than >> described below. You must account for the effect of your new fragments >> on electron density of the entire nanostructure. There is enough >> evidence that an additive approach fails here. >> >> Good luck. >> >> Dr. Vitaly V. Chaban >> >> >> On Mon, Jun 30, 2014 at 11:45 AM, akari karin <j.akarika...@gmail.com> >> wrote: >> > I am trying to simulate carbon nanotubes with some doping. The way i am >> > doping my nanotube is by B-N codoping. >> > >> > i generated the structure but stuck with the topology. i know i need to >> > have the bonded and nonbonded interaction parameters for Boron and >> Nitrogen >> > to do the work but i dont understand how i can get those. >> > >> > i am using the modified oplsaa force field for the simulation of CNT >> > structure. will the default parameters in the oplsaa be okay for my >> > simulation? if not how can i get the parameters? >> > >> > thanks in advance >> > -- >> > 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. >> > > > ------------------------------ > > Message: 5 > Date: Mon, 30 Jun 2014 12:54:42 +0200 > From: "Dr. Vitaly Chaban" <vvcha...@gmail.com> > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] CNT with BN co doping > Message-ID: > <capxdd+b3qaysjc0f7xup6egwwf4eyvj+whuvygwgaj0ldoc...@mail.gmail.com> > Content-Type: text/plain; charset=UTF-8 > > I do not believe that your methodological solution is physically relevant > > Dr. Vitaly V. Chaban > > > On Mon, Jun 30, 2014 at 12:33 PM, akari karin <j.akarika...@gmail.com> > wrote: >> thanks Dr. Vitaly V. Chaban for your reply. >> >> i already simulated the CNT without doping and i have developed a >> structure >> with the doped CNT. >> >> now if i add the dopant atoms in my forcefield file (for example, in my >> case >> i add nonbonded parameters to my ffnonbond.itp and bonded parameters to >> my >> bonded.itp and so on) will it be the correct way to do the simulation? >> >> and it would be very nice if you could explain the statement, >> >> "You must account for the effect of your new fragments on electron >> density >> of the entire nanostructure." >> >> a little bit further. >> >> thanks for your time >> >> >> >> >> On Mon, Jun 30, 2014 at 4:01 PM, Dr. Vitaly Chaban <vvcha...@gmail.com> >> wrote: >>> >>> Simulation of doped nanostructures is much more complicated than >>> described below. You must account for the effect of your new fragments >>> on electron density of the entire nanostructure. There is enough >>> evidence that an additive approach fails here. >>> >>> Good luck. >>> >>> Dr. Vitaly V. Chaban >>> >>> >>> On Mon, Jun 30, 2014 at 11:45 AM, akari karin <j.akarika...@gmail.com> >>> wrote: >>> > I am trying to simulate carbon nanotubes with some doping. The way i >>> > am >>> > doping my nanotube is by B-N codoping. >>> > >>> > i generated the structure but stuck with the topology. i know i need >>> > to >>> > have the bonded and nonbonded interaction parameters for Boron and >>> > Nitrogen >>> > to do the work but i dont understand how i can get those. >>> > >>> > i am using the modified oplsaa force field for the simulation of CNT >>> > structure. will the default parameters in the oplsaa be okay for my >>> > simulation? if not how can i get the parameters? >>> > >>> > thanks in advance >>> > -- >>> > 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. >> >> > > > ------------------------------ > > Message: 6 > Date: Mon, 30 Jun 2014 08:09:39 -0400 > From: Justin Lemkul <jalem...@vt.edu> > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Questions regarding converting .GRO files to > .TOP files > Message-ID: <53b15383.9020...@vt.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > > On 6/29/14, 11:46 PM, Andy Chao wrote: >> Dear GROMACS users: >> >> I have a few questions about converting the .GRO files to .TOP files. I >> first used Python to create a sheet of graphene layer by using the >> following Python codes: >> >> from ase import * >> from ase.structure import graphene_nanoribbon >> from ase io.import* >> gnr1 = graphene_nanoribbon(8,8, type='armchair') >> write('graphene.pdb', gnr1, format='pdb') >> >> Second, I used the following codes to convert the PDB file to GRO file >> for >> the cathode layer: >> >> editconf -f graphene.pdb -o graphene_cathode.gro >> >> Third, I used the following codes to convert the PDB files to GRO file >> for >> the anode layer: >> >> editconf -f graphene.pdb -translate 0 5.0 -o graphene_anode.gro >> >> Fourth, I combined the cathode layer and the anode layer to one complete >> structure according to the following code: >> >> genbox -cs graphene_cathode.gro -cp graphene_anode.gro -maxsol 5000 -box >> 3 >> 1 3 -o electrodes.gro >> >> Fifth, I converted the electrode gro file to top file according to the >> following code: >> >> g_x2top -f electrodes.gro -ff cnt_oplsaa -o device.top >> >> GROMACS showed that there are carbon atoms force field that can not be >> found in the atomname2type.n2t file. >> >> part of the error message is shown as the following: >> >> Can not find forcefield for atom C-447 with 6 bonds >> Can not find forcefield for atom C-448 with 5 bonds.... >> >> Fatal error: >> >> Could only find a forcefield type for 364 out of 512 atoms. >> >> My atomname2type.n2t file consists of the following: >> >> C opls_145 -0.12 12.011 3 C 0.150 C 0.150 H 0.108 >> C opls_145 -0.12 12.011 3 C 0.133 C 0.150 O 0.140 >> C opls_145 0.0 12.011 3 C 0.140 C 0.140 C 0.140 >> C opls_145 0.0 12.011 2 C 0.140 C 0.140 >> >> However, the TOP files for the cathode layer or the anode layer can be >> converted from the GRO files without any error as the following: >> >> g_x2top -f graphene_cathode.gro -ff cnt_oplsaa -o graphene_cathode.top >> g_x2top -f graphene_anode.gro -ff cnt_oplsaa -o graphene_anode.top >> >> can people explain why? What is the reason behind the error message that >> I >> got when converting the GRO file of two combined layer of graphene to the >> TOP file while the same atomname2type.n2t file is used? >> > > The .n2t file assigns bonds for any atoms that satisfy the specified > distance > criteria. The error message indicates that you have some atoms that are > within > bonding range of an unphysical number of bonds. Perhaps the layers are too > > close together or something, but the printed atom numbers should make it > very > easy to identify what is going on simply by visualizing the structure. > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 601 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > ================================================== > > > ------------------------------ > > -- > 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. > > > End of gromacs.org_gmx-users Digest, Vol 122, Issue 128 > ******************************************************* > -- 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.
