[gmx-users] gromacs.org_gmx-users Digest, Vol 122, Issue 128
Andy Chao
achao at energiaq.com
Mon Jun 30 17:11:01 CEST 2014
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-request at maillist.sys.kth.se
<gromacs.org_gmx-users-request at maillist.sys.kth.se> wrote:
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> 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" <vvchaban at gmail.com>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] CNT with BN co doping
> Message-ID:
> <CAPXdD+Yn8ixgXygb9VSiWy41uiZQ5eLnw7m58diHviY_LqhWeg at 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.akarikarin at 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-request at gromacs.org.
>
>
> ------------------------------
>
> Message: 2
> Date: Mon, 30 Jun 2014 12:04:47 +0200
> From: "Dr. Vitaly Chaban" <vvchaban at gmail.com>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] How to calculate Box Vectors in the last line
> of the .gro file?
> Message-ID:
> <CAPXdD+a7q0fMn0MODnthDJB7pnLAJzMGGX6s51uNdpzwWrk2KQ at 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_antoni at 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
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>
>
> ------------------------------
>
> Message: 3
> Date: Mon, 30 Jun 2014 12:10:35 +0200
> From: "Dr. Vitaly Chaban" <vvchaban at gmail.com>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Questions regarding converting .GRO files to
> .TOP files
> Message-ID:
> <CAPXdD+ZUGo0LhLnYejd2h1_mBvAXJCCBaBNdnL0EgZfcJz2MFw at 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 <achao at 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-request at gromacs.org.
>
>
> ------------------------------
>
> Message: 4
> Date: Mon, 30 Jun 2014 16:33:41 +0600
> From: akari karin <j.akarikarin at gmail.com>
> To: gmx-users at gromacs.org, vvchaban at gmail.com
> Subject: Re: [gmx-users] CNT with BN co doping
> Message-ID:
> <CAAiEsOuVdva6ocfbwiDQa8kyF1z7h8nBFjvvbhF0dPTUoobv3Q at 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 <vvchaban at 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.akarikarin at 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-request at 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-request at gromacs.org.
>>
>
>
> ------------------------------
>
> Message: 5
> Date: Mon, 30 Jun 2014 12:54:42 +0200
> From: "Dr. Vitaly Chaban" <vvchaban at gmail.com>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] CNT with BN co doping
> Message-ID:
> <CAPXdD+b3qaySJC0F7XUP6EGWWF4eYVj+WHUVyGWgaJ0LDOcz+g at 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.akarikarin at 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 <vvchaban at 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.akarikarin at 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-request at 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-request at gromacs.org.
>>
>>
>
>
> ------------------------------
>
> Message: 6
> Date: Mon, 30 Jun 2014 08:09:39 -0400
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Questions regarding converting .GRO files to
> .TOP files
> Message-ID: <53B15383.9020503 at 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
>
> jalemkul at 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
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> mail to gmx-users-request at gromacs.org.
>
>
> End of gromacs.org_gmx-users Digest, Vol 122, Issue 128
> *******************************************************
>
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