[gmx-users] RE: gmx-users Digest, Vol 94, Issue 24

Fri Feb 3 10:06:41 CET 2012

Dear All,

I found a strange thing about VMD. When I use mouse label residue from graph (Mouse --> Label --> Atom), i would get a correct residue as it is in .gro file, while when I use graphics --> representations --> selections, then the residue selected here is totally different with the one which has the same number in the .gro file.

Be careful with it, everybody.
Jiangfeng. 

    Jiangfeng Du, PhD Student
    Cardiovascular Research Institute Maastricht
    Department of Biochemistry
    P.O. Box 616
    Mobile: +31-681741859
    FAX: +31-43-3884159
    6200 MD Maastricht
    The Netherlands
________________________________________
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Subject: gmx-users Digest, Vol 94, Issue 24

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Today's Topics:

   1. Re: Mass fraction (Steven Neumann)
   2. Re: g_dist (Justin A. Lemkul)
   3. Orders of the residues in gromacs (Du Jiangfeng (BIOCH))
   4. Re: Orders of the residues in gromacs (Justin A. Lemkul)
   5. g_dist (dina dusti)
   6. Re: g_dist (Mark Abraham)
   7. Re: Mass fraction (Mark Abraham)
   8. Re: Orders of the residues in gromacs (Jianguo Li)

----------------------------------------------------------------------

Message: 1
Date: Thu, 2 Feb 2012 16:22:34 +0000
From: Steven Neumann <s.neumann08 at gmail.com>
Subject: [gmx-users] Re: Mass fraction
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID:
        <CAKZJqQEKdJso-3Ta6X8o_hyfVSPpa8n-SZVTFVdiO33-=1P9ZA at mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"

Anyone can help? Please...

On Thu, Feb 2, 2012 at 1:51 PM, Steven Neumann <s.neumann08 at gmail.com>wrote:

> Dear Gmx Users,
>
> My system consists of Protein attached to the surface (water solution)
> I am trying to calculate equilibrium distance - dependent (from my
> surface) distributions of residues (e.g. polar) in my system collected in
> the mass fraction. So in this case I am interested in only one coordinate
> (X) which perpendicular to my surface. I assume to use just last 5-10 ns
> (out of 100ns) as an equilibrium.
>
> Is there any way to use g_rdf for this purpose?
>
> Or shall I use g_dist, calculate distances of each residue (e.g. from
> polar residues) for last 5-10 ns, take X coordinate, average it over time
> and multiply by its mass?
>
> Do you have any suggestions?
>
> Thank you,
>
> Steven
>
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Message: 2
Date: Thu, 02 Feb 2012 11:34:08 -0500
From: "Justin A. Lemkul" <jalemkul at vt.edu>
Subject: Re: [gmx-users] g_dist
To: dina dusti <dinadusti at yahoo.com>,   Discussion list for GROMACS
        users <gmx-users at gromacs.org>
Message-ID: <4F2ABB00.40801 at vt.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

dina dusti wrote:
> Dear Prof
>
> Thank you very much from your response.
> She said me:
> "In g_dist, when you select two groups for distance calculation, it
> computes the distance between COM's of groups. Now, what is expected for
> the distance between the micelle's COM and the COM of (e.g.) head
> groups? Clearly, it's near zero ! So you should first calculate the
> distance for each group separately and then average over all distances."
>
> But I didn't understand what was her mean about "you should first
> calculate the distance for each group separately and then average over
> all distances.", because I did g_dist between micelle and for example
> head group and then used g_analyze for dist.xvg and I had the quantity
> near zero!!!
>

Which is precisely what she told you.  Her suggestion is to measure the
head-tail distance of each molecule separately, then average.  This will require
a large number of index groups (2 groups per molecule, multiplied by however
many molecules you have to deal with) and will be very tedious, but it can be
done in this manner.

-Justin

--
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================

------------------------------

Message: 3
Date: Thu, 2 Feb 2012 18:16:10 +0100
From: "Du Jiangfeng (BIOCH)" <j.du at maastrichtuniversity.nl>
Subject: [gmx-users] Orders of the residues in gromacs
To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
Message-ID:
        <020E61ECF99C7B45AA1627BB541D3A9207403629DD at UM-MAIL4111.unimaas.nl>
Content-Type: text/plain; charset="us-ascii"

Dear Friends,

I want to measure some data of a special residue, for instance TRP143, from my MD result. But i encountered a problem.

The residue number 143 is ordered in .gro file, while it seems the residue orders is random in gromacs. It points to another residue when I specify residue number 143 in VMD or when I am using make_ndx program ( --> r 143; q). Apparently, gromacs numbering system is not based on the orders in the .gro structure file.

Does anybody know how to link the gromacs order to the structure file's order correctly?

Thank you in advance,

Jiangfeng.

    Jiangfeng Du, PhD Student
    Cardiovascular Research Institute Maastricht
    Department of Biochemistry
    P.O. Box 616
    Mobile: +31-681741859
    FAX: +31-43-3884159
    6200 MD Maastricht
    The Netherlands

------------------------------

Message: 4
Date: Thu, 02 Feb 2012 12:43:17 -0500
From: "Justin A. Lemkul" <jalemkul at vt.edu>
Subject: Re: [gmx-users] Orders of the residues in gromacs
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <4F2ACB35.8050808 at vt.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

Du Jiangfeng (BIOCH) wrote:
> Dear Friends,
>
> I want to measure some data of a special residue, for instance TRP143, from my MD result. But i encountered a problem.
>
> The residue number 143 is ordered in .gro file, while it seems the residue orders is random in gromacs. It points to another residue when I specify residue number 143 in VMD or when I am using make_ndx program ( --> r 143; q). Apparently, gromacs numbering system is not based on the orders in the .gro structure file.
>
> Does anybody know how to link the gromacs order to the structure file's order correctly?
>

Depending on the Gromacs version you're using, residue numbering is treated
differently.  In pdb2gmx, you can choose to renumber the residues from 1 or not.
  The default is to not renumber the file.  You should check to see what you did
with respect to this option and whether or not your coordinate file is numbered
from 1.  If it is not, then what you think is residue 143 may not be interpreted
that way by all external programs, depending on whether or not they respect the
numbering of the .gro file.

-Justin

--
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================

------------------------------

Message: 5
Date: Thu, 2 Feb 2012 10:56:34 -0800 (PST)
From: dina dusti <dinadusti at yahoo.com>
Subject: [gmx-users] g_dist
To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
Message-ID:
        <1328208994.86661.YahooMailNeo at web121301.mail.ne1.yahoo.com>
Content-Type: text/plain; charset="us-ascii"

Dear Prof.

Thank you very much from your help.

Best Regards
Dina
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Message: 6
Date: Fri, 03 Feb 2012 09:52:27 +1100
From: Mark Abraham <Mark.Abraham at anu.edu.au>
Subject: Re: [gmx-users] g_dist
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <4F2B13AB.1040600 at anu.edu.au>
Content-Type: text/plain; charset="iso-8859-1"

On 3/02/2012 3:17 AM, dina dusti wrote:
> Dear Prof
>
> Thank you very much from your response.
> She said me:
> "In g_dist, when you select two groups for distance calculation, it
> computes the distance between COM's of groups. Now, what is expected
> for the distance between the micelle's COM and the COM of (e.g.) head
> groups? Clearly, it's near zero ! So you should first calculate the
> distance for each group separately and then average over all distances."
>
> But I didn't understand what was her mean about "you should first
> calculate the distance for each group separately and then average over
> all distances.", because I did g_dist between micelle and for example
> head group and then used g_analyze for dist.xvg and I had the quantity
> near zero!!!
>

This can be done more efficiently with g_bond, treating each
head-to-tail distance as a "bond".

Mark
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Message: 7
Date: Fri, 03 Feb 2012 09:53:15 +1100
From: Mark Abraham <Mark.Abraham at anu.edu.au>
Subject: Re: [gmx-users] Mass fraction
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <4F2B13DB.1070503 at anu.edu.au>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

On 3/02/2012 12:51 AM, Steven Neumann wrote:
> Dear Gmx Users,
> My system consists of Protein attached to the surface (water solution)
> I am trying to calculate equilibrium distance - dependent (from my
> surface) distributions of residues (e.g. polar) in my system collected
> in the mass fraction. So in this case I am interested in only one
> coordinate (X) which perpendicular to my surface. I assume to use just
> last 5-10 ns (out of 100ns) as an equilibrium.
> Is there any way to use g_rdf for this purpose?
> Or shall I use g_dist, calculate distances of each residue (e.g. from
> polar residues) for last 5-10 ns, take X coordinate, average it over
> time and multiply by its mass?
>

This seems fine.

Mark

------------------------------

Message: 8
Date: Fri, 3 Feb 2012 10:04:28 +0800 (SGT)
From: Jianguo Li <ljggmx at yahoo.com.sg>
Subject: Re: [gmx-users] Orders of the residues in gromacs
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID:
        <1328234668.1600.YahooMailNeo at web190204.mail.sg3.yahoo.com>
Content-Type: text/plain; charset="iso-8859-1"

Another possible reason is due to vmd, which numbers the residue from 0. Residue 143 in gromacs corresponds to residue 142 in vmd.
Cheers,

Jianguo

________________________________
 From: Du Jiangfeng (BIOCH) <j.du at maastrichtuniversity.nl>
To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
Sent: Friday, 3 February 2012, 1:16
Subject: [gmx-users] Orders of the residues in gromacs