[gmx-users] gromacs.org_gmx-users Digest, Vol 185, Issue 50
Nirali Desai
nirali.d.imsc14 at ahduni.edu.in
Sun Sep 15 12:09:53 CEST 2019
>
> Hello,
>
Thank you so much. I have taken two groups at a time only and calculated
the energies (Defining using index). My question is if I have done it for
the two groups 1. AB 2. C. Does that energy also include the intramolecular
interaction energy of A & B?.
Please guide me on this.
Sorry for the inconvenience.
Thanking you,
Nirali Desai
>
> Message: 1
> Date: Sat, 14 Sep 2019 23:39:25 +0500
> From: Najamuddin Memon <najamuddinmemon63 at gmail.com>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Regarding obtaining potential energy using
> energy groups
> Message-ID:
> <
> CALwxfCLEfpByDPDwkRQwPVY0+-10Yq4BRq3wSyF4FDDV2xYL5w at mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> No you should take two groups at a time
> Like A VS B then A vs C and so on before doing energy analysis you should
> make index file that you have to call in command line with -n index.ndx
> Regards
> Najam
>
> On Fri, Sep 13, 2019, 3:21 PM Nirali Desai <nirali.d.imsc14 at ahduni.edu.in>
> wrote:
>
> > Dear all
> > I have a system with 3 protein chains A B and C. I want to calculate the
> > potential energy between different chains.
> > I created energy groups by creating a new index file.
> > If I calculate potential energy between C as one group and (AB) as
> another
> > group, will it contain the potential energy of interaction between A and
> B
> > too?
> >
> > Your kind guidance in this matter is highly appreciated.
> >
> >
> > Thanking you,
> > Nirali Desai
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
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> > send a mail to gmx-users-request at gromacs.org.
> >
>
>
> ------------------------------
>
> Message: 2
> Date: Sun, 15 Sep 2019 00:57:15 +0530
> From: Nashit Jalal 17250017 <nashit.jalal at iitgn.ac.in>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Regarding obtaining potential energy using
> energy groups
> Message-ID:
> <
> CAFy6K6Aj6dojzr1WCWUNLOpp1ZYA7G0-u+XrJh3X_cR0zGNxUg at mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> I think so that the question is to confirm whether finding potential energy
> making (AB) and C as 2 groups similar to the potential energy obtained by
> adding energies obtained by making A -C and B -C as groups
>
> -Nashit
>
> On Sun, Sep 15, 2019 at 12:10 AM Najamuddin Memon <
> najamuddinmemon63 at gmail.com> wrote:
>
> > No you should take two groups at a time
> > Like A VS B then A vs C and so on before doing energy analysis you should
> > make index file that you have to call in command line with -n index.ndx
> > Regards
> > Najam
> >
> > On Fri, Sep 13, 2019, 3:21 PM Nirali Desai <
> nirali.d.imsc14 at ahduni.edu.in>
> > wrote:
> >
> > > Dear all
> > > I have a system with 3 protein chains A B and C. I want to calculate
> the
> > > potential energy between different chains.
> > > I created energy groups by creating a new index file.
> > > If I calculate potential energy between C as one group and (AB) as
> > another
> > > group, will it contain the potential energy of interaction between A
> and
> > B
> > > too?
> > >
> > > Your kind guidance in this matter is highly appreciated.
> > >
> > >
> > > Thanking you,
> > > Nirali Desai
> > > --
> > > 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
> >
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> > send a mail to gmx-users-request at gromacs.org.
> >
>
>
> ------------------------------
>
> Message: 3
> Date: Sun, 15 Sep 2019 04:59:53 +0800
> From: "=?gb18030?B?WkhBTkcgQ2hlbmc=?=" <272699575 at qq.com>
> To: "=?gb18030?B?Z3JvbWFjcy5vcmdfZ214LXVzZXJz?="
> <gromacs.org_gmx-users at maillist.sys.kth.se>
> Subject: [gmx-users] What is the equivalent command for
> insert-molecules in Gromacs 3.3.1?
> Message-ID: <tencent_8DCC0A1ED147271FFEAE8A171738D289A006 at qq.com>
> Content-Type: text/plain; charset="gb18030"
>
> Dear All,
>
>
> Due to a software that is only compatible to Version 3.3.1, I have to use
> that to prepare the simulation box. I was told "command not found? when
> using the insert-molecules.
>
>
> So what should I do to put multiple molecules in a box?
>
>
> Thank you!
>
>
> Cheng
>
> ------------------------------
>
> Message: 4
> Date: Sun, 15 Sep 2019 02:32:37 +0500
> From: Najamuddin Memon <najamuddinmemon63 at gmail.com>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Regarding obtaining potential energy using
> energy groups
> Message-ID:
> <CALwxfCLNWec-JPq3Ykgbs24AyzRKw+WkOLxWZ=
> 7WSA3eD2yPwA at mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> It depends on interaction of proteins i.e A interacts with B
> A&B both interact with C
> Only A or only B interacts with C
> In 2nd option you can make one group (A&B) and 2nd group as C
>
> On Sun, Sep 15, 2019, 12:28 AM Nashit Jalal 17250017 <
> nashit.jalal at iitgn.ac.in> wrote:
>
> > I think so that the question is to confirm whether finding potential
> energy
> > making (AB) and C as 2 groups similar to the potential energy obtained by
> > adding energies obtained by making A -C and B -C as groups
> >
> > -Nashit
> >
> > On Sun, Sep 15, 2019 at 12:10 AM Najamuddin Memon <
> > najamuddinmemon63 at gmail.com> wrote:
> >
> > > No you should take two groups at a time
> > > Like A VS B then A vs C and so on before doing energy analysis you
> should
> > > make index file that you have to call in command line with -n index.ndx
> > > Regards
> > > Najam
> > >
> > > On Fri, Sep 13, 2019, 3:21 PM Nirali Desai <
> > nirali.d.imsc14 at ahduni.edu.in>
> > > wrote:
> > >
> > > > Dear all
> > > > I have a system with 3 protein chains A B and C. I want to calculate
> > the
> > > > potential energy between different chains.
> > > > I created energy groups by creating a new index file.
> > > > If I calculate potential energy between C as one group and (AB) as
> > > another
> > > > group, will it contain the potential energy of interaction between A
> > and
> > > B
> > > > too?
> > > >
> > > > Your kind guidance in this matter is highly appreciated.
> > > >
> > > >
> > > > Thanking you,
> > > > Nirali Desai
> > > > --
> > > > 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.
> > >
> > --
> > 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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> > send a mail to gmx-users-request at gromacs.org.
> >
>
>
> ------------------------------
>
> Message: 5
> Date: Sun, 15 Sep 2019 08:56:36 +0200
> From: David van der Spoel <spoel at xray.bmc.uu.se>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Regarding obtaining potential energy using
> energy groups
> Message-ID: <fab2b70a-d9de-6a09-defe-9829ac0f9c35 at xray.bmc.uu.se>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
> Den 2019-09-14 kl. 23:32, skrev Najamuddin Memon:
> > It depends on interaction of proteins i.e A interacts with B
> > A&B both interact with C
> > Only A or only B interacts with C
> > In 2nd option you can make one group (A&B) and 2nd group as C
>
> Note that this only tells you about non-bonded interaction at short
> range. In order to also include the long range (PME), checkout this
> paper: J. Chem. Theor. Comput. 9 pp. 4542-4551 (2013) (supporting info
> in particular).
> Then you still do not have grouped energies for the bonded forces since
> this is not implemented and finally you have to ask yourself what does
> an interaction energy mean?
>
> >
> > On Sun, Sep 15, 2019, 12:28 AM Nashit Jalal 17250017 <
> > nashit.jalal at iitgn.ac.in> wrote:
> >
> >> I think so that the question is to confirm whether finding potential
> energy
> >> making (AB) and C as 2 groups similar to the potential energy obtained
> by
> >> adding energies obtained by making A -C and B -C as groups
> >>
> >> -Nashit
> >>
> >> On Sun, Sep 15, 2019 at 12:10 AM Najamuddin Memon <
> >> najamuddinmemon63 at gmail.com> wrote:
> >>
> >>> No you should take two groups at a time
> >>> Like A VS B then A vs C and so on before doing energy analysis you
> should
> >>> make index file that you have to call in command line with -n index.ndx
> >>> Regards
> >>> Najam
> >>>
> >>> On Fri, Sep 13, 2019, 3:21 PM Nirali Desai <
> >> nirali.d.imsc14 at ahduni.edu.in>
> >>> wrote:
> >>>
> >>>> Dear all
> >>>> I have a system with 3 protein chains A B and C. I want to calculate
> >> the
> >>>> potential energy between different chains.
> >>>> I created energy groups by creating a new index file.
> >>>> If I calculate potential energy between C as one group and (AB) as
> >>> another
> >>>> group, will it contain the potential energy of interaction between A
> >> and
> >>> B
> >>>> too?
> >>>>
> >>>> Your kind guidance in this matter is highly appreciated.
> >>>>
> >>>>
> >>>> Thanking you,
> >>>> Nirali Desai
> >>>> --
> >>>> 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.
> >>>
> >> --
> >> 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.
> >>
>
>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Head of Department, Cell & Molecular Biology, Uppsala University.
> Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
> http://www.icm.uu.se
>
>
> --
>
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