Dear Justin,
For example, In hemoglobin (A-H helix), the particular E and F helix gets
moved during the MD simulation, I would like to calculate this helix
movements/rotation angle? Thanks.
You'll have to define what you mean by "helix movements." Everything moves in a
simulation, but what is it that you're trying to quantify? If it's secondary
structure itself, use do_dssp. If you're after something else, you will have to
be more specific
-----------------------Original Message-----------------------
From: gmx-users-requ...@gromacs.org
To: gmx-users@gromacs.org
Sent date: 2013-01-17 22:02:54 GMT +0900 (ROK)
Subject: gmx-users Digest, Vol 105, Issue 88
Send gmx-users mailing list submissions to
gmx-users@gromacs.org
To subscribe or unsubscribe via the World Wide Web, visit
http://lists.gromacs.org/mailman/listinfo/gmx-users
or, via email, send a message with subject or body 'help' to
gmx-users-requ...@gromacs.org
You can reach the person managing the list at
gmx-users-ow...@gromacs.org
When replying, please edit your Subject line so it is more specific
than "Re: Contents of gmx-users digest..."
Today's Topics:
1. Re: Re: Simulation of 2D lattice model (Bogdan Costescu)
2. conversion of Gromacs trajectories (rhombic dodecahedric) and
topologies to Amber format (Anna Marabotti)
3. Re: conversion of Gromacs trajectories (rhombic dodecahedric)
and topologies to Amber format (Justin Lemkul)
4. Re: conversion of Gromacs trajectories (rhombic dodecahedric)
and topologies to Amber format (Daniel Larsson)
5. Movements of secondary structure (?????)
6. Re: Re: Simulation of 2D lattice model (James Starlight)
7. Re: Movements of secondary structure (Justin Lemkul)
----------------------------------------------------------------------
Message: 1
Date: Thu, 17 Jan 2013 12:03:46 +0100
From: Bogdan Costescu <bcoste...@gmail.com>
Subject: Re: [gmx-users] Re: Simulation of 2D lattice model
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Message-ID:
<cah+wpduv-uyezfoz7cjrzj_-5mjruur5j8qjtoshoodg9jm...@mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1
On Thu, Jan 17, 2013 at 10:59 AM, James Starlight
<jmsstarli...@gmail.com> wrote:
> thank you for so detailed explanation.
You're welcome. Now it's up to you to use it :)
> Now it's only intresting to me
> if it possible to change vdw radius (assuming it as the distance from
> center of atom to it outer electronic shell)?
Yes, it's possible.
> E.g I want to change
> such value for each node in my lattice model (e.g for CH2 united atom
> that value might be > 1.5 and I want dicrease it to the 1 A ( as for
> simple carbon). Might I do it via some simplest modifications in the
> nonbonded.itp or should I do that by means of changes in
> sigma/epsillon terms (Which I also must express from A(c6) and B(c12)
> based on gromac's combination rules) ?
If nonbonded.itp for your chosen force field is expressed in
sigma/epsilon (I guess that this is the case because you talk about an
existing value for sigma), then it's only a matter of changing the
sigma parameter of that atomic species.
Keep in mind that this is only a description of the change - it
doesn't guarantee that the change is valid. If I'd be a reviewer I'd
ask for a reason for changing one of the parameters (sigma) and
keeping the other (epsilon) constant.
Cheers,
Bogdan
------------------------------
Message: 2
Date: Thu, 17 Jan 2013 12:22:02 +0100
From: Anna Marabotti <amarabo...@unisa.it>
Subject: [gmx-users] conversion of Gromacs trajectories (rhombic
dodecahedric) and topologies to Amber format
To: gmx-users@gromacs.org
Message-ID: <50f7deda.5090...@unisa.it>
Content-Type: text/plain; charset=ISO-8859-15; format=flowed
Dear all,
we'd need to convert a trajectory in .xtc format (and the related
topology file) to a format that could be read by Amber program (I'd need
to perform MM-PBSA calculations).
We tried to do it using VMD, but failed to produce a correct trajectory
to be read by MMPBSA.py tool. It complains about the fact that it
expected only 3 or 6 box coords, but I ran the trajectory using a
rhombic dodecahedric box, with 9 box coords.
I read the gmx-user archive to find hints to overcome the problem, but
only found incomplete, and in some cases quite old, suggestions (We are
currently using Gromacs 4.5.4 version). I don't see anywhere a detailed
suggestion on how to proceed, and I have even the doubt that this is not
possible to do.
Could you please give me some information about, possibly with detailed
descriptions about the commands and the flags to use?
Many thanks in advance for your kind answer and best regards
Anna
--
______________________________________________
Anna Marabotti, Ph.D.
Assistant Professor
Department of Chemistry and Biology
University of Salerno
Via Ponte don Melillo
84084 Fisciano (SA)
Italy
Phone: +39 089 969583
Fax: +39 089 969603
E-mail: amarabo...@unisa.it
Skype: annam1972
"When a man with a gun meets a man with a pen, the man with the gun is a dead
man"
(Roberto Benigni, about Roberto Saviano)
------------------------------
Message: 3
Date: Thu, 17 Jan 2013 06:27:04 -0500
From: Justin Lemkul <jalem...@vt.edu>
Subject: Re: [gmx-users] conversion of Gromacs trajectories (rhombic
dodecahedric) and topologies to Amber format
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Message-ID: <50f7e008.20...@vt.edu>
Content-Type: text/plain; charset=ISO-8859-15; format=flowed
On 1/17/13 6:22 AM, Anna Marabotti wrote:
> Dear all,
> we'd need to convert a trajectory in .xtc format (and the related topology
> file)
> to a format that could be read by Amber program (I'd need to perform MM-PBSA
> calculations).
> We tried to do it using VMD, but failed to produce a correct trajectory to be
> read by MMPBSA.py tool. It complains about the fact that it expected only 3
> or 6
> box coords, but I ran the trajectory using a rhombic dodecahedric box, with 9
> box coords.
> I read the gmx-user archive to find hints to overcome the problem, but only
> found incomplete, and in some cases quite old, suggestions (We are currently
> using Gromacs 4.5.4 version). I don't see anywhere a detailed suggestion on
> how
> to proceed, and I have even the doubt that this is not possible to do.
> Could you please give me some information about, possibly with detailed
> descriptions about the commands and the flags to use?
>
You can write a new box using trjconv and make it whatever you want.
Presumably
you're stripping out water and such anyway, so all you would have to do is
center your solute in whatever box you want:
trjconv -s topol.tpr -f traj.xtc -center -box x y z
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
------------------------------
Message: 4
Date: Thu, 17 Jan 2013 13:05:33 +0100
From: Daniel Larsson <lars...@xray.bmc.uu.se>
Subject: Re: [gmx-users] conversion of Gromacs trajectories (rhombic
dodecahedric) and topologies to Amber format
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Message-ID: <76bf68c1-279f-459d-9997-753779807...@xray.bmc.uu.se>
Content-Type: text/plain; charset=us-ascii
On Jan 17, 2013, at 12:27 , Justin Lemkul wrote:
>
>
> On 1/17/13 6:22 AM, Anna Marabotti wrote:
>> Dear all,
>> we'd need to convert a trajectory in .xtc format (and the related topology
>> file)
>> to a format that could be read by Amber program (I'd need to perform MM-PBSA
>> calculations).
>> We tried to do it using VMD, but failed to produce a correct trajectory to be
>> read by MMPBSA.py tool. It complains about the fact that it expected only 3
>> or 6
>> box coords, but I ran the trajectory using a rhombic dodecahedric box, with 9
>> box coords.
>> I read the gmx-user archive to find hints to overcome the problem, but only
>> found incomplete, and in some cases quite old, suggestions (We are currently
>> using Gromacs 4.5.4 version). I don't see anywhere a detailed suggestion on
>> how
>> to proceed, and I have even the doubt that this is not possible to do.
>> Could you please give me some information about, possibly with detailed
>> descriptions about the commands and the flags to use?
The "magic bullet" for converting rhombic dodecahedron box trajectories into
something that makes intuitive sense is to use trjconv with the flags -ur
compact and -pbc mol. Then trjconv will pick the periodic copy of each molecule
that has its mass center the closest to the box center instead of the default
of choosing the periodic image that has the mass center inside of the triclinic
box.
> You can write a new box using trjconv and make it whatever you want.
> Presumably you're stripping out water and such anyway, so all you would have
> to do is center your solute in whatever box you want:
>
> -Justin
I agree with Justin. It is probably best to strip of all water and create a new
box if amber cannot understand triclinic boxes.
Use the -center or the -fit flag if the solute diffuses out from the original
periodic copy of the box. (But be wary to use -fit with operations that rotate
the box!) I recommend that you save the original trajectory.
Daniel
------------------------------
Message: 5
Date: Thu, 17 Jan 2013 21:37:22 +0900 (KST)
From: ????? <ra...@kaist.ac.kr>
Subject: [gmx-users] Movements of secondary structure
To: gmx-users@gromacs.org
Message-ID: <50f7f09d3fe2_@_imoxion.com>
Content-Type: text/plain; charset="UTF-8"
Dear all,
I have been trying to calculate and plot the secondary structure of helix
movements during the simulation on time through g_helix, g_helix orient,
g_principle and g_mindist but none of them shown the helix movements.
Is there any other tool can elaborate the helix movements ? Plz suggestion are
appreciated.
------------------------------
Message: 6
Date: Thu, 17 Jan 2013 16:51:53 +0400
From: James Starlight <jmsstarli...@gmail.com>
Subject: Re: [gmx-users] Re: Simulation of 2D lattice model
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Message-ID:
<caalqopzkpwf2csm_0gr+om6vcffhofdfa41kj_apohwl81-...@mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1
Bogdan,
thanks againfor explanation.
So if I have force field with the C6/C12 terms (instead of
sigma\epsilon) I need to express sigma (which correspond to the Rmin
in LJ equation) as the (C12/C6)^0.5. Than if I want to increase sigma
( and consequently to increase vdw radius of my atom) I must to
increase c12 or decreace C6 terms. Does it correct in general ?
2013/1/17 Bogdan Costescu <bcoste...@gmail.com>:
> On Thu, Jan 17, 2013 at 10:59 AM, James Starlight
> <jmsstarli...@gmail.com> wrote:
>> thank you for so detailed explanation.
>
> You're welcome. Now it's up to you to use it :)
>
>> Now it's only intresting to me
>> if it possible to change vdw radius (assuming it as the distance from
>> center of atom to it outer electronic shell)?
>
> Yes, it's possible.
>
>> E.g I want to change
>> such value for each node in my lattice model (e.g for CH2 united atom
>> that value might be > 1.5 and I want dicrease it to the 1 A ( as for
>> simple carbon). Might I do it via some simplest modifications in the
>> nonbonded.itp or should I do that by means of changes in
>> sigma/epsillon terms (Which I also must express from A(c6) and B(c12)
>> based on gromac's combination rules) ?
>
> If nonbonded.itp for your chosen force field is expressed in
> sigma/epsilon (I guess that this is the case because you talk about an
> existing value for sigma), then it's only a matter of changing the
> sigma parameter of that atomic species.
>
> Keep in mind that this is only a description of the change - it
> doesn't guarantee that the change is valid. If I'd be a reviewer I'd
> ask for a reason for changing one of the parameters (sigma) and
> keeping the other (epsilon) constant.
>
> Cheers,
> Bogdan
> --
> gmx-users mailing list gmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
------------------------------
Message: 7
Date: Thu, 17 Jan 2013 08:01:25 -0500
From: Justin Lemkul <jalem...@vt.edu>
Subject: Re: [gmx-users] Movements of secondary structure
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Message-ID: <50f7f625.2030...@vt.edu>
Content-Type: text/plain; charset=UTF-8; format=flowed
On 1/17/13 7:37 AM, ��������������� wrote:
> Dear all,
>
> I have been trying to calculate and plot the secondary structure of helix
> movements during the simulation on time through g_helix, g_helix orient,
> g_principle and g_mindist but none of them shown the helix movements.
>
> Is there any other tool can elaborate the helix movements ? Plz suggestion
> are appreciated.
>
You'll have to define what you mean by "helix movements." Everything moves in
a
simulation, but what is it that you're trying to quantify? If it's secondary
structure itself, use do_dssp. If you're after something else, you will have
to
be more specific.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
------------------------------
--
gmx-users mailing list
gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
End of gmx-users Digest, Vol 105, Issue 88
******************************************
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
