[gmx-users] Regarding calculating energy autocorrelation function
ravikumarvenkatraman
ravikumarvenkatraman at gmail.com
Thu May 15 08:05:52 CEST 2014
Dear Gromacs user's,
Could anybody tell me how to calculate energy autocorrelation function using Gromacs. I need it to take statistically uncorrelated snapshots for further calculations or somebody has done the same using some other method that is available in gromacs will also suffice.
Thank you
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-------- Original message --------
From: gromacs.org_gmx-users-request at maillist.sys.kth.se
Date: 15/05/2014 09:21 (GMT+05:30)
To: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: gromacs.org_gmx-users Digest, Vol 121, Issue 66
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Today's Topics:
1. Re: Ion concentration of genion vs charmm-gui (Ali Khan)
2. amber to gromacs conversion (Chetan Mahajan)
3. amber to gromacs conversion of LJ potential (Chetan Mahajan)
4. Re: amber to gromacs conversion of LJ potential (Justin Lemkul)
5. flat-bottomed potentials (ANDRES ADOLFO ORTEGA GUERRERO)
6. Re: Why does the list keep unsubscribing me? (X Rules)
----------------------------------------------------------------------
Message: 1
Date: Wed, 14 May 2014 13:15:29 -0400
From: Ali Khan <akk5r at virginia.edu>
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Ion concentration of genion vs charmm-gui
Message-ID:
<CA+h7WiXLkG5iae7XME3rwwePd3ppqEEQW5ZvUuz8v5=PF=bjUw at mail.gmail.com>
Content-Type: text/plain; charset=UTF-8
I just did. It turns out that when there is a charged lipid in the system
(as in my case), charmm-gui increases the effective concentration to
compensate for the system's net charge. I have pasted my discourse with
them below.
My email:
I have a question. I generated a membrane using the charmm-gui membrane
builder. The server generated a 2POPC:1POPS bilayer in a box with water.
The box dimensions were 135.355 A x 135.355 A x 130 A. I asked membrane
builder to added 140 mM KCl, and it recommended 232 positive ions and 46
negative ions. I also made this ion calculation by hand using the volume of
the box, and my calculation gave me 201 positive ions for 0.14 M. If I
calculated the concentration of ions based solely on the amount of water
molecules in the box (54682 water molecules), I obtain 139 positive ions to
make 0.14 M. I am trying to figure out where is the discrepancy is.
Reply:
The discrepancy arises from the net charge of the system since you have PS
lipid types. So, your effective concentration should be higher to
compensate such system net charge.
On Wed, May 14, 2014 at 1:04 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 5/14/14, 12:06 PM, Ali Khan wrote:
>
>> By hand it is about 201 molecules. It is strange that the membrane builder
>> in charmm-gui gives a different answer for the same box dimensions. I
>> guess
>> those of us that use the charmm-gui membrane builder should keep this in
>> mind.
>>
>>
> Better yet, please report it to the CHARMM-GUI people. If there's
> something wrong, it needs to be fixed. There is a very easy email form to
> fill out to report issues.
>
> -Justin
>
>
>
>> On Wed, May 14, 2014 at 11:14 AM, Erik Marklund <
>> erik.marklund at chem.ox.ac.uk
>>
>>> wrote:
>>>
>>
>> Hi Ali,
>>>
>>> And what would you expect in this case, based on the definition of
>>> concentration?
>>>
>>> Erik
>>>
>>> On 14 May 2014, at 04:11, Ali Khan <akk5r at virginia.edu> wrote:
>>>
>>> Sorry Mark,
>>>>
>>>> I did not mean 201, 000 atoms; I meant 201 potassium atoms vs 232
>>>>
>>> potassium
>>>
>>>> atoms. Its a small difference, and both methods have the same box size.
>>>>
>>>>
>>>> On Tue, May 13, 2014 at 3:38 PM, Mark Abraham <mark.j.abraham at gmail.com
>>>> wrote:
>>>>
>>>> Sounds like a problem for a high-school chemistry test ;-)
>>>>>
>>>> concentration =
>>>
>>>> quantity / volume. From the factor of ~1000, probably you're inputting
>>>>>
>>>> box
>>>
>>>> sizes in A instead of nm, or vice-versa, somewhere.
>>>>>
>>>>> Mark
>>>>>
>>>>>
>>>>> On Tue, May 13, 2014 at 8:43 PM, Ali Khan <akk5r at virginia.edu> wrote:
>>>>>
>>>>> Hey,
>>>>>>
>>>>>> I generated a membrane in charmm-gui that I will be simulating in
>>>>>>
>>>>> gromacs.
>>>>>
>>>>>> I am using genion to add 0.14 M potassium by using the -conc flag. In
>>>>>> a
>>>>>>
>>>>> box
>>>>>
>>>>>> with dimensions 13.5355 nm x 13.5355 nm x 13 nm, genion states that I
>>>>>> should add 201 K atoms. When I constructed the system in charmm-gui,
>>>>>>
>>>>> the
>>>
>>>> server stated that I should add 232 potassium ions to reach a 0.14 M
>>>>>> concentration. Does anyone have a suggestion of which potassium ion
>>>>>>
>>>>> number
>>>>>
>>>>>> I should go with?
>>>>>>
>>>>>> Best Wishes,
>>>>>> Ali Khan
>>>>>> --
>>>>>> Gromacs Users mailing list
>>>>>>
>>>>>> * Please search the archive at
>>>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>>>>> posting!
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>>>>>> send a mail to gmx-users-request at gromacs.org.
>>>>>>
>>>>>> --
>>>>> Gromacs Users mailing list
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> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
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>
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------------------------------
Message: 2
Date: Wed, 14 May 2014 19:15:16 -0500
From: Chetan Mahajan <chetanvm10 at gmail.com>
To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
Subject: [gmx-users] amber to gromacs conversion
Message-ID:
<CAEYgXrbSon9_Sp_J574D43O9gubf0rkd=K-QPy5vc06Uk+Lhaw at mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
Dear All,
While converting LJ parameters from Amber to Gromacs, acpype tool (that is
used for converting Amber input files into those for gromacs) uses
following form:
sigma = 2 * r * 2^(-1/6)
I understand the factor 2^(-1/6), but there is another "2" that appears in
the beginning. Where is that factor coming from? That factor does not arise
when we choose following forms for LJ potential functions in Amber as well
as Gromacs.
Amber:
[image: Inline image 1]
Gromacs:
[image: Inline image 2]
Thanks in advance!
regards
Chetan
------------------------------
Message: 3
Date: Wed, 14 May 2014 19:21:20 -0500
From: Chetan Mahajan <chetanvm10 at gmail.com>
To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
Subject: [gmx-users] amber to gromacs conversion of LJ potential
Message-ID:
<CAEYgXrZHShuupKwZBqHqh7uHj60pV+h1dQXwhEYOOT6hHyJiQw at mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
Dear All,
While converting LJ parameters from Amber to Gromacs, acpype tool (that is
used for converting Amber input files into those for gromacs) uses
following form:
sigma = 2 * r * 2^(-1/6)
I understand the factor 2^(-1/6), but there is another "2" that appears in
the beginning. Where is that factor coming from? That factor does not arise
when we choose following forms for LJ potential functions in Amber as well
as Gromacs.
Amber:
[image: Inline image 1]
Gromacs:
[image: Inline image 2]
Thanks in advance!
regards
Chetan
------------------------------
Message: 4
Date: Wed, 14 May 2014 20:22:41 -0400
From: Justin Lemkul <jalemkul at vt.edu>
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] amber to gromacs conversion of LJ potential
Message-ID: <537408D1.5070708 at vt.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
On 5/14/14, 8:21 PM, Chetan Mahajan wrote:
> Dear All,
>
> While converting LJ parameters from Amber to Gromacs, acpype tool (that is
> used for converting Amber input files into those for gromacs) uses
> following form:
>
> sigma = 2 * r * 2^(-1/6)
>
> I understand the factor 2^(-1/6), but there is another "2" that appears in
> the beginning. Where is that factor coming from? That factor does not arise
> when we choose following forms for LJ potential functions in Amber as well
> as Gromacs.
>
IIRC, Amber stores values in its parameter files as Rmin/2, hence the need to
multiply by 2.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
------------------------------
Message: 5
Date: Wed, 14 May 2014 21:25:27 -0500
From: ANDRES ADOLFO ORTEGA GUERRERO
<andres.ortega at correounivalle.edu.co>
To: "gromacs.org_gmx-users at maillist.sys.kth.se"
<gromacs.org_gmx-users at maillist.sys.kth.se>
Subject: [gmx-users] flat-bottomed potentials
Message-ID:
<CAA0WmSsjgPL6F+LOcTrpx1iiB6CEPdPP__wmA0ALh+0F36Qi4w at mail.gmail.com>
Content-Type: text/plain; charset=UTF-8
Hi Dear Gromacs Users,
I am running a umbrella samplimg simulation with gromacs 4.6.5, this
simulations is a molecule permeating an ion channel, i decided to use X Y
position restraints 400KJ , but i
am not pretty sure if this kind of bias if a real mistake, i was wondering
if anyone know how to use de fbposred function (bondfree.c) from gromacs 5,
in order to use it with gromacs 4.6.5, in order to get a Flat bottomed
potential ,
Because i dont want to affect to much my PMF calculation
Thanks in advace
------------------------------
Message: 6
Date: Thu, 15 May 2014 03:51:37 +0000
From: X Rules <xrules at live.com>
To: gmx <gmx-users at gromacs.org>
Subject: Re: [gmx-users] Why does the list keep unsubscribing me?
Message-ID: <BLU178-W30875BA922E4136A416F0DA6360 at phx.gbl>
Content-Type: text/plain; charset="iso-8859-1"
Thanks for the explanation Rossen.I hope mailman gets some more artificial intelligence in coming future :).cheers,Abhi
> Date: Wed, 14 May 2014 14:33:00 +0200
> From: rossen at kth.se
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Why does the list keep unsubscribing me?
>
> Hi,
>
> Someone else mentioned the same recently.
>
> Automatic removal can happen if someone, e.g. a spammer, sends a mail to
> gmx-users-unsubscribe at gromacs.org while faking your email address in the
> From: field.
>
> Mailman is now maintained centrally by the university, so I can't dig in
> the logs for more information.
>
> Rossen
>
> On 14/05/14 10:29, X Rules wrote:
> > This is the second time in 2 months, that I am unsubscribed from the list and i have to subscribe again. I just get an email that you have been unsubscribed from the list?
> > How can I get unsubscribed without my intervention is beyond understanding?
> >
> >
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
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------------------------------
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