[gmx-users] gromacs.org_gmx-users Digest, Vol 136, Issue 19
PAVAN PAYGHAN
pavanapex at gmail.com
Wed Aug 5 13:10:25 CEST 2015
Dear Tsjerk,
Thanks a lot for your reply. It was really helpful.
However it does not answer what I am looking for.
1. I want to calculate changes in the form of distance along the entire
trajectory as if I am fitting all the frames and then calculating the
changes for the same atom (or residue).
2. As I am checking the distance changes for same atom (or residue) is
there any way I can answer this using gromacs tools or any other method in
your knowledge?
Thanks a lot in Advance,
Pavan Payghan
On Wed, Aug 5, 2015 at 1:22 PM, <
gromacs.org_gmx-users-request at maillist.sys.kth.se> wrote:
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> Today's Topics:
>
> 1. Re: how to calculate ESP at certain position (Zhenyu Meng)
> (Groenhof, Gerrit)
> 2. 1, 3-dipalmitoyl-2-oleoyl parameterization based on Berger
> lipid parameters (Anna M?ller)
> 3. Re: calculating single atom changes along the trajectory as a
> measure of distance (Tsjerk Wassenaar)
> 4. Re: how to calculate ESP at certain position (Zhenyu Meng)
> (Zhenyu Meng)
> 5. forming disulfide linkage between two chains (tasneem kausar)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 5 Aug 2015 06:45:52 +0000
> From: "Groenhof, Gerrit" <ggroenh at gwdg.de>
> To: "gromacs.org_gmx-users at maillist.sys.kth.se"
> <gromacs.org_gmx-users at maillist.sys.kth.se>
> Subject: Re: [gmx-users] how to calculate ESP at certain position
> (Zhenyu Meng)
> Message-ID:
> <858A7947BC0FE04DA05E1786A6D51D4509E99519 at um-excdag-a05.um.gwdg.de
> >
> Content-Type: text/plain; charset="us-ascii"
>
>
> 5. Re: how to calculate ESP at certain position (Zhenyu Meng)
>
> Haven't given it much thought, but if it is only one or few locations
> you're interested in, can't you simply place a +1 e charged dummy atom at
> that location in your system and re-compute the total electrostatic energy?
>
> To correct for the self interaction of that probe charge, you could
> subtract the total electrostatic energy of the point charge alone in the
> same periodic box.
>
> Gerrit
>
>
>
>
> M
> Message: 5
> Date: Wed, 5 Aug 2015 10:00:10 +0800
> From: Zhenyu Meng <fdmm1989 at gmail.com>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] how to calculate ESP at certain position
> Message-ID:
> <CAJffFwaSp5gHL6pEjvgJyFsJxTdM=
> 9CWGGvOpQ6UpbutaNv1cg at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Dear Andre,
> Thanks a lot for your advice.
> I ask this question because I read a related paper which use point-charge
> potential: ?=4???qi/ri .
> I'm very curious about how it could fulfill this since they mention they
> use GROMACS but according to my knowledge GROMACS does not have such a
> tool.
> So I suppose they write their own code.
> Here is the link of the paper:
> http://pubs.acs.org/doi/abs/10.1021/jp803661f
>
>
>
> 2015-08-04 21:30 GMT+08:00 Andr? Farias de Moura <moura at ufscar.br>:
>
> > Dear Zhenyu,
> >
> > I would be careful with the choice of words: you cannot say that a point
> in
> > space has an electrostatic potential without saying where you have set
> the
> > reference electrostatic potential to zero (it is a relative quantity, not
> > absolute).
> >
> > I never used the spherical version of g_potential myself, but assuming it
> > does what my lab made code does, you will get a profile of V(r) around
> the
> > COM of the reference group and the value at the COM should always be
> > compared with the values of the surrounding spherical layers, so you will
> > be able to state that the electrostatic potential is either higher or
> lower
> > at that point with respect with a reference position in the radial
> profile
> > (your choice).
> >
> > Also mind that the COM is not an actual point, you are performing a
> > numerical double integration of the charge density between r and r+dr, so
> > the COM is actually a small sphere. Being small, I do not think that
> > instantaneous calculation of electrostatic potential would make any sense
> > at all, the region around the COM is always the region where the
> potential
> > takes longer to converge (tens of nanoseconds in my case). This is not an
> > artifact of the program: parallel layers along one direction of the box
> > have the same volume and are sampled with the same statistical precision,
> > whereas spherical layers have increasing volumes as we move from the COM,
> > meaning that statistical sampling is very poor at the COM as compared to
> > the outer layers (I would expect wild oscillations without physical
> > significance at the origin of the profile).
> >
> > best
> >
> > Andre
> >
> > On Tue, Aug 4, 2015 at 12:58 AM, Zhenyu Meng <fdmm1989 at gmail.com> wrote:
> >
> > > Dear all,
> > > I want to calculate electrostatic potential at a certain position in a
> > box.
> > > I check the available tools and found only g_potential is related with
> > > this.
> > > However g_potential give the graph of potential vs. box length(may be z
> > > axis).
> > > So my first question: Is this potential value the potential at the COM
> of
> > > the group I select?
> > > Second question: how can I calculate the potential at certain position
> > vs.
> > > time?
> > >
> > > --
> > > Sincerely,
> > > Mr. Meng Zhenyu
> > > Division of Chemistry and Biological Chemistry
> > > School of Physical and Mathematical Sciences
> > > Nanyang Technological University
> > > --
> > > 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.
> > >
> >
> >
> >
> > --
> > _____________
> >
> > Prof. Dr. Andr? Farias de Moura
> > Department of Chemistry
> > Federal University of S?o Carlos
> > S?o Carlos - Brazil
> > phone: +55-16-3351-8090
> > --
> > 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.
>
>
>
>
> --
> Sincerely,
> Mr. Meng Zhenyu
> Division of Chemistry and Biological Chemistry
> School of Physical and Mathematical Sciences
> Nanyang Technological University
>
>
> ------------------------------
>
>
>
> ------------------------------
>
> Message: 2
> Date: Wed, 5 Aug 2015 08:58:58 +0200
> From: Anna M?ller <anna.moeller at tum.de>
> To: "gromacs.org_gmx-users at maillist.sys.kth.se"
> <gromacs.org_gmx-users at maillist.sys.kth.se>
> Subject: [gmx-users] 1, 3-dipalmitoyl-2-oleoyl parameterization based
> on Berger lipid parameters
> Message-ID: <735A6C13-ABF4-42EC-B657-D415AA311128 at tum.de>
> Content-Type: text/plain; charset=utf-8
>
> Hello gmx-users,
>
> I am parameterizing a 1,3-dipalmitoyl-2-oleoyl TAG based on Berger Lipid
> parameters.
> While creating an itp file on the bases of a dppc.itp file with Berger
> lipid parameters, I?m challenged with the correct charges on the CH1-OA-C=O
> charge group.
>
> onhttp://
> www.researchgate.net/post/How_do_you_parametrize_Trilinolein_based_on_Berger_lipid_parameters_when_you_have_itp_and_gro_of_your_molecule_from_PRODRG
>
> I already found an explanation on how to charge the group, but I?m not
> quite sure how the rest of the group is charged, if the ester O is charged
> with -0.7.
>
> The -CH2-(C=O)-O- charge group has the following charges:
> CH2 0.5 ; O ester -0.7; carbonyl C 0.8 and carbonyl O -0.6
>
> Any help would be appreciated!
>
> Best regards
>
> Anna
>
> ------------------------------
>
> Message: 3
> Date: Wed, 5 Aug 2015 09:22:12 +0200
> From: Tsjerk Wassenaar <tsjerkw at gmail.com>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] calculating single atom changes along the
> trajectory as a measure of distance
> Message-ID:
> <
> CABzE1Sh6iCuH1OGiqik0rxznD7gX+KFhys_LY2vNfDgUcWxbNw at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi Pavan,
>
> The distance from an atom to itself is zero by definition. Also, distance
> in only defined between things, so, indeed, you need two groups for gmx
> dist. If you mean distance over PBC it's a different matter. Then you want
> the distance between a group and any of its periodic images. That's what
> gmx mindist is for. If it's the position you need, then you want gmx traj.
>
> Hope it helps,
>
> Tsjerk
> On Aug 5, 2015 08:34, "PAVAN PAYGHAN" <pavanapex at gmail.com> wrote:
>
> > Dear Groamcs Users,
> >
> > I am in need to calculate distance changes for a single atom (same atom)
> > along the simulation time.
> > I tried to do so using g_dist by giving input of same atom index group
> > twice for the calculation, output was in null values, which can not be
> > true.
> > To my surprise g_dist needs two different groups in order to calculate
> > distance vs Time changes.
> > Is there any tool or method available in gromacs for doing such
> > calculation??
> >
> > 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: 4
> Date: Wed, 5 Aug 2015 15:37:26 +0800
> From: Zhenyu Meng <fdmm1989 at gmail.com>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] how to calculate ESP at certain position
> (Zhenyu Meng)
> Message-ID:
> <CAJffFwZ1C0P2d1koBdiOhdaYbfSztrncv_hTPuvuH+i=
> WXVYZQ at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Dear Prof. Groenhof,
> Your suggestion sounds enlightening, I can give it a try.
> Thank you!
>
> 2015-08-05 14:45 GMT+08:00 Groenhof, Gerrit <ggroenh at gwdg.de>:
>
> >
> > 5. Re: how to calculate ESP at certain position (Zhenyu Meng)
> >
> > Haven't given it much thought, but if it is only one or few locations
> > you're interested in, can't you simply place a +1 e charged dummy atom at
> > that location in your system and re-compute the total electrostatic
> energy?
> >
> > To correct for the self interaction of that probe charge, you could
> > subtract the total electrostatic energy of the point charge alone in the
> > same periodic box.
> >
> > Gerrit
> >
> >
> >
> >
> > M
> > Message: 5
> > Date: Wed, 5 Aug 2015 10:00:10 +0800
> > From: Zhenyu Meng <fdmm1989 at gmail.com>
> > To: gmx-users at gromacs.org
> > Subject: Re: [gmx-users] how to calculate ESP at certain position
> > Message-ID:
> > <CAJffFwaSp5gHL6pEjvgJyFsJxTdM=
> > 9CWGGvOpQ6UpbutaNv1cg at mail.gmail.com>
> > Content-Type: text/plain; charset=UTF-8
> >
> > Dear Andre,
> > Thanks a lot for your advice.
> > I ask this question because I read a related paper which use point-charge
> > potential: ?=4???qi/ri .
> > I'm very curious about how it could fulfill this since they mention they
> > use GROMACS but according to my knowledge GROMACS does not have such a
> > tool.
> > So I suppose they write their own code.
> > Here is the link of the paper:
> > http://pubs.acs.org/doi/abs/10.1021/jp803661f
> >
> >
> >
> > 2015-08-04 21:30 GMT+08:00 Andr? Farias de Moura <moura at ufscar.br>:
> >
> > > Dear Zhenyu,
> > >
> > > I would be careful with the choice of words: you cannot say that a
> point
> > in
> > > space has an electrostatic potential without saying where you have set
> > the
> > > reference electrostatic potential to zero (it is a relative quantity,
> not
> > > absolute).
> > >
> > > I never used the spherical version of g_potential myself, but assuming
> it
> > > does what my lab made code does, you will get a profile of V(r) around
> > the
> > > COM of the reference group and the value at the COM should always be
> > > compared with the values of the surrounding spherical layers, so you
> will
> > > be able to state that the electrostatic potential is either higher or
> > lower
> > > at that point with respect with a reference position in the radial
> > profile
> > > (your choice).
> > >
> > > Also mind that the COM is not an actual point, you are performing a
> > > numerical double integration of the charge density between r and r+dr,
> so
> > > the COM is actually a small sphere. Being small, I do not think that
> > > instantaneous calculation of electrostatic potential would make any
> sense
> > > at all, the region around the COM is always the region where the
> > potential
> > > takes longer to converge (tens of nanoseconds in my case). This is not
> an
> > > artifact of the program: parallel layers along one direction of the box
> > > have the same volume and are sampled with the same statistical
> precision,
> > > whereas spherical layers have increasing volumes as we move from the
> COM,
> > > meaning that statistical sampling is very poor at the COM as compared
> to
> > > the outer layers (I would expect wild oscillations without physical
> > > significance at the origin of the profile).
> > >
> > > best
> > >
> > > Andre
> > >
> > > On Tue, Aug 4, 2015 at 12:58 AM, Zhenyu Meng <fdmm1989 at gmail.com>
> wrote:
> > >
> > > > Dear all,
> > > > I want to calculate electrostatic potential at a certain position in
> a
> > > box.
> > > > I check the available tools and found only g_potential is related
> with
> > > > this.
> > > > However g_potential give the graph of potential vs. box length(may
> be z
> > > > axis).
> > > > So my first question: Is this potential value the potential at the
> COM
> > of
> > > > the group I select?
> > > > Second question: how can I calculate the potential at certain
> position
> > > vs.
> > > > time?
> > > >
> > > > --
> > > > Sincerely,
> > > > Mr. Meng Zhenyu
> > > > Division of Chemistry and Biological Chemistry
> > > > School of Physical and Mathematical Sciences
> > > > Nanyang Technological University
> > > > --
> > > > 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.
> > > >
> > >
> > >
> > >
> > > --
> > > _____________
> > >
> > > Prof. Dr. Andr? Farias de Moura
> > > Department of Chemistry
> > > Federal University of S?o Carlos
> > > S?o Carlos - Brazil
> > > phone: +55-16-3351-8090
> > > --
> > > 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.
> >
> >
> >
> >
> > --
> > Sincerely,
> > Mr. Meng Zhenyu
> > Division of Chemistry and Biological Chemistry
> > School of Physical and Mathematical Sciences
> > Nanyang Technological University
> >
> >
> > ------------------------------
> >
> > --
> > 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.
> >
>
>
>
> --
> Sincerely,
> Mr. Meng Zhenyu
> Division of Chemistry and Biological Chemistry
> School of Physical and Mathematical Sciences
> Nanyang Technological University
>
>
> ------------------------------
>
> Message: 5
> Date: Wed, 5 Aug 2015 13:22:53 +0530
> From: tasneem kausar <tasneemkausar12 at gmail.com>
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: [gmx-users] forming disulfide linkage between two chains
> Message-ID:
> <
> CAFaK4UYcbrVDwJd8HF0qiHQ8hxohz0Uvc7SUZ3kA3gjX+-Ev5Q at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> sir
>
> I am trying to make disulfide linkage between chain A and B.
> The command line is "pdb2gmx -f prtn.pdb -o prtn.gro -p prtn.top -ss.
> I have used -ss option of pdb2gmx but disufide linkage is not formed
> between the chains A and B.
> What is the possible way to form the disulfide linkage in Gromacs usind the
> pdb2gmx.
> Please resolve the issue
>
>
> 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.
>
> End of gromacs.org_gmx-users Digest, Vol 136, Issue 19
> ******************************************************
>
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