[gmx-users] Re: gmx-users Digest, Vol 97, Issue 69
farideh zergani
farideh_zergani at yahoo.com
Thu May 10 14:29:43 CEST 2012
________________________________
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Subject: gmx-users Digest, Vol 97, Issue 69
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Today's Topics:
1. Re: Charge derrivation for OPLSAA forcefield (Dommert Florian)
2. Restraining atoms (Steven Neumann)
3. Re: Restraining atoms (Justin A. Lemkul)
4. genconf -trj?!? (Faezeh Kargar)
5. Re: genconf -trj?!? (Justin A. Lemkul)
6. Free energy calculation about ions (hope Justin A. Lemkul can
give some suggestions ) (DeChang Li)
7. Treating solute as a rigid body with flexible solvent
molecules (Debayan Chakraborty)
----------------------------------------------------------------------
Message: 1
Date: Wed, 09 May 2012 17:32:52 +0200
From: Dommert Florian <dommert at icp.uni-stuttgart.de>
Subject: Re: [gmx-users] Charge derrivation for OPLSAA forcefield
To: Milinda Samaraweera <milinda49 at yahoo.com>, Discussion list for
GROMACS users <gmx-users at gromacs.org>
Message-ID: <1336577572.2383.109.camel at fermi>
Content-Type: text/plain; charset="utf-8"
On Tue, 2012-05-08 at 11:38 -0700, Milinda Samaraweera wrote:
> Hi Guys
>
>
> I was using the program http://q4md-forcefieldtools.org/RED/ to
> derrive ESP based charges for some molecules that I study. Is this a
> correct method to do so if not please let me know what are the other
> methods that are available.
>
Hi,
this is really a hard questions to answer. Different methods to derive
partial charges are present, which rely on various ideas. Actually, the
partial charges of a force field should be consistent, because they are
anyway just an approximation for the true charge density. Common force
fields like AMBER or OPLS-AA were constructed with different
consideration, giving rise to the differences, though they allow to
desribe the same molecules. So I would study, how the remaining
parameters of the applied force field were derived. Furthermore be aware
that altering a single charge of force field might require readaption of
dihedral and LJ parameters. Hence, always be careful and benchmark the
force field against single as well collective static and dynamic
properties, carefully.
/Flo
>
> thanks alot
>
> Milinda Samaraweera
> University of Connecticut
> Department of Chemistry
> 55 N Eagleville road
> unit 3060
> Storrs CT
> USA
> --
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--
Florian Dommert
Dipl. - Phys.
Institute for Computational Physics
University Stuttgart
Pfaffenwaldring 27
70569 Stuttgart
EMail: dommert at icp.uni-stuttgart.de
Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert
Tel.: +49 - (0)711 - 68563613
Fax.: +49 - (0)711 - 68563658
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Message: 2
Date: Wed, 9 May 2012 16:34:19 +0100
From: Steven Neumann <s.neumann08 at gmail.com>
Subject: [gmx-users] Restraining atoms
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID:
<CAKZJqQH2mAYnHD-dxeZ2Vioz38334HNFLiq74QwxR5VeGEmuYg at mail.gmail.com>
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Dear Gmx Users,
My plane surface is made of atoms. I would like to restrain positions
between them so they will move all togehter or create bonds between them.
Would you advise how to do this in the easiest way?
Steven
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Message: 3
Date: Wed, 09 May 2012 11:37:17 -0400
From: "Justin A. Lemkul" <jalemkul at vt.edu>
Subject: Re: [gmx-users] Restraining atoms
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <4FAA8F2D.1090302 at vt.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
On 5/9/12 11:34 AM, Steven Neumann wrote:
> Dear Gmx Users,
>
> My plane surface is made of atoms. I would like to restrain positions between
> them so they will move all togehter or create bonds between them. Would you
> advise how to do this in the easiest way?
>
If you need to "restrain positions" then you need [position_restraints]. The
form of the restraints follows from the structure of the topology.
Also note that you cannot create bonds in a classical MD simulation. If you
need to maintain some distances, then use actual bonds or [distance_restraints].
-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: 4
Date: Wed, 9 May 2012 20:29:25 +0430
From: "Faezeh Kargar" <f_kargar at iasbs.ac.ir>
Subject: [gmx-users] genconf -trj?!?
To: gmx-users at gromacs.org
Message-ID:
<df3ffa6c05dd26ab8426f09fe809a18b.squirrel at mail.iasbs.ac.ir>
Content-Type: text/plain; charset="utf-8"
Dear all,
my coarse grained simulations contain a cubic box
with 16 peptides. After 85ns peptides aggregate but because of PBC I
have problem in analyzing some data like radius of gyration and
clustering. I searched mailing list to solve this problem by trjconv. I
examined its different options but without any results. casually
genconf came in my mind. I want to use this command for a trajectory
with option -trj
genconf -f .tpr -trj .xtc/.gro -o .gro -nbox 2 1
1
but when I use it I face with "Segmentation
fault". I searched mailing list and found just one
question"http://lists.gromacs.org/pipermail/gmx-users/2004-July/011196.html"
whithout answer.
Please guide me wheather this command can help me to generate an
aggregated system for analyzing? If Yes, How? If No help me
please?Thank you in advance
Faezeh Kargar
--
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Message: 5
Date: Wed, 09 May 2012 12:54:28 -0400
From: "Justin A. Lemkul" <jalemkul at vt.edu>
Subject: Re: [gmx-users] genconf -trj?!?
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <4FAAA144.9030707 at vt.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
On 5/9/12 11:59 AM, Faezeh Kargar wrote:
>
> Dear all,
>
> my coarse grained simulations contain a cubic box with 16 peptides. After 85ns
> peptides aggregate but because of PBC I have problem in analyzing some data like
> radius of gyration and clustering. I searched mailing list to solve this problem
> by trjconv. I examined its different options but without any results. casually
> genconf came in my mind. I want to use this command for a trajectory with option
> -trj
>
> genconf -f .tpr -trj .xtc/.gro -o .gro -nbox 2 1 1
>
> but when I use it I face with "Segmentation fault". I searched mailing list and
> found just one
> question"http://lists.gromacs.org/pipermail/gmx-users/2004-July/011196.html"
> whithout answer.
>
It's almost certainly a bug, but the fact that no one has asked about the -trj
option in nearly eight years suggests it's probably not a high priority to fix,
or simply that no one ever noticed it. In any case, genconf is not likely to be
a suitable solution.
> Please guide me wheather this command can help me to generate an aggregated
> system for analyzing? If Yes, How? If No help me please?
>
You need trjconv, and likely several instances of it. Complex systems like
these require great care and potentially custom index groups. There is a
generic trjconv workflow here:
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions#Suggested_trjconv_workflow
There are also numerous posts in the list archive regarding clustering of
various molecules, including peptides and micelles. The tips there will likely
guide you, but if you need further help you'll need to provide explicit commands
that you've tried, what they produced, and why it's not what you're after. The
solution is in trjconv, but without knowing what you've tried, it's hard to
provide additional help.
-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: 6
Date: Thu, 10 May 2012 10:37:11 +0800
From: DeChang Li <li.dc06 at gmail.com>
Subject: [gmx-users] Free energy calculation about ions (hope Justin
A. Lemkul can give some suggestions )
To: gmx-users at gromacs.org
Message-ID:
<CAB0HCkKS3j5X_v9Bzj7Uoi68UH=YczjtamcqSZAAq3Jjt4+89g at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1
Dear all,
I want to calculate the ion solvation free energy (e.g. an ion
Na+ solvated in a water box) using Bennett Acceptance Ratio (BAR)
method, following the tutorial by Justin A. Lemkul. However, if I turn
off the Coulombic interaction, the total charge of my system would not
neutral at all. Does this affact my calculation?
=========================================
Dechang Li , Ph.D
Biomechanics and Biomaterials Laboratory
Department of Applied Mechanics
School of Aerospace Engineering
Beijing Institute of Technology
Beijing 100081, P. R. China
=========================================
------------------------------
Message: 7
Date: Thu, 10 May 2012 14:59:58 +0530
From: Debayan Chakraborty <debayan.ch at gmail.com>
Subject: [gmx-users] Treating solute as a rigid body with flexible
solvent molecules
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID:
<CALU3VhKbAiPhsORcoj50+UxPD4gyG4SDsa23gKW+acY7CpQwhg at mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"
Dear Gromacs Users,
I want to simulate an organic dye in a
solvent ( such as aniline as DMA). I have already relaxed the solvent
around the dye in the equilibration run ( NPT) using position restraints
on the solute. Now for the production run I want to release the position
restraints on the dye and allow it to translate and rotate like a rigid
body under the influence of the solvent. I am new to GROMACS, and I am not
sure what is the best way to realise this. Any help would be greatly
appreciated.
Best Regards,
Debayan Chakraborty
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