# [gmx-users] RE: gmx-users Digest, Vol 105, Issue 88

라지브간디 rajiv at kaist.ac.kr
Fri Jan 18 02:42:07 CET 2013

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-request at gromacs.org
To: gmx-users at 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 at 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-request at gromacs.org

You can reach the person managing the list at

gmx-users-owner at gromacs.org

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 <bcostescu at gmail.com>

Subject: Re: [gmx-users] Re: Simulation of 2D lattice model

To: Discussion list for GROMACS users <gmx-users at gromacs.org>

Message-ID:

<CAH+WPduV-UyEzFOz7cJRzJ_-5mjRUUR5j8QjtOSHoOdg9jMu2g at mail.gmail.com>

Content-Type: text/plain; charset=ISO-8859-1

On Thu, Jan 17, 2013 at 10:59 AM, James Starlight

<jmsstarlight at 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 <amarabotti at unisa.it>

Subject: [gmx-users] conversion of Gromacs trajectories (rhombic

dodecahedric) and topologies to Amber format

To: gmx-users at gromacs.org

Message-ID: <50F7DEDA.5090903 at 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.

descriptions about the commands and the flags to use?

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: amarabotti at 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"

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

Message: 3

Date: Thu, 17 Jan 2013 06:27:04 -0500

From: Justin Lemkul <jalemkul at 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 at gromacs.org>

Message-ID: <50F7E008.20100 at 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

Subject: Re: [gmx-users] conversion of Gromacs trajectories (rhombic

dodecahedric) and topologies to Amber format

To: Discussion list for GROMACS users <gmx-users at gromacs.org>

Message-ID: <76BF68C1-279F-459D-9997-753779807F3A at 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: ????? <rajiv at kaist.ac.kr>

Subject: [gmx-users] Movements of secondary structure

To: gmx-users at gromacs.org

Message-ID: <50f7f09d3fe2_ at _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 <jmsstarlight at gmail.com>

Subject: Re: [gmx-users] Re: Simulation of 2D lattice model

To: Discussion list for GROMACS users <gmx-users at gromacs.org>

Message-ID:

<CAALQopzkpwF2CSm_0Gr+om6VcffHofDFA41Kj_APohWL81-Hqw at 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 <bcostescu at gmail.com>:

> On Thu, Jan 17, 2013 at 10:59 AM, James Starlight

> <jmsstarlight at 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 at 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-request at 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 <jalemkul at vt.edu>

Subject: Re: [gmx-users] Movements of secondary structure

To: Discussion list for GROMACS users <gmx-users at gromacs.org>

Message-ID: <50F7F625.2030103 at 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 at 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

******************************************