> > 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 <najamuddinmemo...@gmail.com> > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Regarding obtaining potential energy using > energy groups > Message-ID: > < > calwxfclefpbydpdwkrqwpvy0+-10yq4brq3wsyf4fddv2xy...@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.ims...@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-requ...@gromacs.org. > > > > > ------------------------------ > > Message: 2 > Date: Sun, 15 Sep 2019 00:57:15 +0530 > From: Nashit Jalal 17250017 <nashit.ja...@iitgn.ac.in> > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Regarding obtaining potential energy using > energy groups > Message-ID: > < > cafy6k6aj6dojzr1wcwunlopp1zya7g0-u+xrjh3x_cr0zgn...@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 < > najamuddinmemo...@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.ims...@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-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: 3 > Date: Sun, 15 Sep 2019 04:59:53 +0800 > From: "=?gb18030?B?WkhBTkcgQ2hlbmc=?=" <272699...@qq.com> > To: "=?gb18030?B?Z3JvbWFjcy5vcmdfZ214LXVzZXJz?=" > <gromacs.org_gmx-users@maillist.sys.kth.se> > Subject: [gmx-users] What is the equivalent command for > insert-molecules in Gromacs 3.3.1? > Message-ID: <tencent_8dcc0a1ed147271ffeae8a171738d289a...@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 <najamuddinmemo...@gmail.com> > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Regarding obtaining potential energy using > energy groups > Message-ID: > <CALwxfCLNWec-JPq3Ykgbs24AyzRKw+WkOLxWZ= > 7wsa3ed2y...@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.ja...@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 < > > najamuddinmemo...@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.ims...@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-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. > > > > > -- > > 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: Sun, 15 Sep 2019 08:56:36 +0200 > From: David van der Spoel <sp...@xray.bmc.uu.se> > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Regarding obtaining potential energy using > energy groups > Message-ID: <fab2b70a-d9de-6a09-defe-9829ac0f9...@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.ja...@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 < > >> najamuddinmemo...@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.ims...@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-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. > >>> > >> -- > >> 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. > >> > > > -- > 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 > > > -- > -- 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.