[gmx-users] RE: Re: Wierd results from Umbrella sampling (lloyd riggs)
Du Jiangfeng (BIOCH)
j.du at maastrichtuniversity.nl
Mon May 21 09:26:18 CEST 2012
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Today's Topics:
1. Re: forcefields for lipids (Peter C. Lai)
2. Re: Wierd results from Umbrella sampling (lloyd riggs)
3. Re: forcefields for lipids (Justin A. Lemkul)
4. Re: forcefields for lipids (Thomas Piggot)
5. Re: forcefields for lipids (Shima Arasteh)
6. PMF profile from Umbrella - Plateau (Steven Neumann)
----------------------------------------------------------------------
Message: 1
Date: Wed, 16 May 2012 08:06:25 -0500
From: "Peter C. Lai" <pcl at uab.edu>
Subject: Re: [gmx-users] forcefields for lipids
To: <gmx-users at gromacs.org>
Message-ID: <20120516130624.GI94109 at cesium.hyperfine.info>
Content-Type: text/plain; charset="iso-8859-1"
Off the top of my head:
There are the Berger lipids for the gromos FFs (Justin's tutorial)
There was a B2 Adrenergic receptor paper that used Amber.
and of course Martini appears to be everyone's favorite coarse grain FF.
The literature search shall be left as an exercise for the reader.
(You can even use google to search this mailing list or mirrors of it)
On 2012-05-16 05:59:22AM -0700, Shima Arasteh wrote:
> Dear gmx users,
>
> Which force fields are suggested for lipids? Except CHARMM, any other forcefields?
> Anybody may suggest me articles in this about?
>
>
> Thanks in advance
>
> ?
> Sincerely,
> Shima
> --
> gmx-users mailing list gmx-users at gromacs.org
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==================================================================
Peter C. Lai | University of Alabama-Birmingham
Programmer/Analyst | KAUL 752A
Genetics, Div. of Research | 705 South 20th Street
pcl at uab.edu | Birmingham AL 35294-4461
(205) 690-0808 |
==================================================================
------------------------------
Message: 2
Date: Wed, 16 May 2012 15:15:47 +0200
From: "lloyd riggs" <lloyd.riggs at gmx.ch>
Subject: Re: [gmx-users] Wierd results from Umbrella sampling
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <20120516131547.182840 at gmx.net>
Content-Type: text/plain; charset="utf-8"
Hi Steve,
Thank you for your reply. I checked the trajectory but they are in the simulation box. There is indeed some negative energy in some samplings, but even that it should not make the total energy goes to zero, that is weird.
Jiang.
One thought from justins post in the past,
Look at the .trj in VMD with the unit cell box and see if something sticks out at the end (ie comes up in the bootmn of the box from the top). It then does what you show, however it may not be that. If it is, you'll have to increase your box deminsion in the pull dir. and re-run it or throw out the data after it turns negative...
Steve
-------- Original-Nachricht --------
> Datum: Wed, 16 May 2012 10:08:06 +0200
> Von: "Du Jiangfeng (BIOCH)" <j.du at maastrichtuniversity.nl>
> An: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
> Betreff: [gmx-users] Wierd results from Umbrella sampling
> Dear Sir/Madam,
>
> I have performed umbrella pulling and umbrella sampling my protein from a
> DOPC/DOPS membrane. Unfortunately, the results are really bad (Energy curve
> suddenly turns to zero at the last 1 nm) and the histograph does not show
> any overlap. Actually, I did it strictly based on Justin's tutorial, with
> the sample spacing of 0.2 nm.
>
> Here are some lines from the end of the energy file (The energy should not
> decrease since it was in summation):
>
> Distance(nm) Energy (Kcal/mol)
> 5.288348 5.705318e+01
> 5.316250 4.881724e+01
> 5.344152 4.022505e+01
> 5.372054 3.101854e+01
> 5.399956 2.208200e+01
> 5.427858 1.343340e+01
> 5.455761 4.267619e+00
> 5.483663 -5.084078e+00 ? minus
> 5.511565 -1.486168e+01 ? minus
> 5.539467 -2.393515e+01 ? minus
> 5.567369 -3.343453e+01 ? minus
>
>
> Followings are some lines from the end of histograph file:
>
> Distance(nm)
> 5.455761 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8
> 5.483663 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8
> 5.511565 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12
> 5.539467 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4
> 5.567369 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2
>
>
> I am really depressed because it took me quiet a long time to sampling but
> it seems in vain... I really no idea to find out what went wrong.
>
> I am looking forward to your help. Thanks a lot.
>
> 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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------------------------------
Message: 3
Date: Wed, 16 May 2012 09:18:52 -0400
From: "Justin A. Lemkul" <jalemkul at vt.edu>
Subject: Re: [gmx-users] forcefields for lipids
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <4FB3A93C.8020104 at vt.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
On 5/16/12 9:06 AM, Peter C. Lai wrote:
> Off the top of my head:
> There are the Berger lipids for the gromos FFs (Justin's tutorial)
> There was a B2 Adrenergic receptor paper that used Amber.
> and of course Martini appears to be everyone's favorite coarse grain FF.
>
There is also an OPLS-AA formulation of lipid parameters, and ways to combine
OPLS-AA representations of proteins with the Berger lipids.
-Justin
> The literature search shall be left as an exercise for the reader.
> (You can even use google to search this mailing list or mirrors of it)
>
> On 2012-05-16 05:59:22AM -0700, Shima Arasteh wrote:
>> Dear gmx users,
>>
>> Which force fields are suggested for lipids? Except CHARMM, any other forcefields?
>> Anybody may suggest me articles in this about?
>>
>>
>> Thanks in advance
>>
>>
>> Sincerely,
>> Shima
>
>> --
>> 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
>
>
--
========================================
Justin A. Lemkul, Ph.D.
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, 16 May 2012 14:25:26 +0100
From: Thomas Piggot <t.piggot at soton.ac.uk>
Subject: Re: [gmx-users] forcefields for lipids
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <4FB3AAC6.70402 at soton.ac.uk>
Content-Type: text/plain; charset="ISO-8859-1"; format=flowed
Hi,
In addition to the ones already mentioned (CHARMM, GAFF/AMBER, Berger,
OPLS-AA) there are several united-atom GROMOS based lipid forcefields
(43A1-S3, 53A6L/54A7, 53A6 Kukol, etc.). The Lipidbook website is a
useful place to find lots of lipid parameters in one location:
http://lipidbook.bioch.ox.ac.uk/
The choice of force field will depend upon what you wish to simulate.
With PC lipids there are more force fields available compared to other
phospholipids, so your choice of lipid may dictate your choice of force
field. Additionally some of the available lipid force fields may work
well for one type of lipid but not another. Finally if you have a
membrane-protein system you also need to consider the combination with
an appropriate protein force field.
Cheers
Tom
Peter C. Lai wrote:
> Off the top of my head:
> There are the Berger lipids for the gromos FFs (Justin's tutorial)
> There was a B2 Adrenergic receptor paper that used Amber.
> and of course Martini appears to be everyone's favorite coarse grain FF.
>
> The literature search shall be left as an exercise for the reader.
> (You can even use google to search this mailing list or mirrors of it)
>
> On 2012-05-16 05:59:22AM -0700, Shima Arasteh wrote:
>> Dear gmx users,
>>
>> Which force fields are suggested for lipids? Except CHARMM, any other forcefields?
>> Anybody may suggest me articles in this about?
>>
>>
>> Thanks in advance
>>
>>
>> Sincerely,
>> Shima
>
>> --
>> 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
>
>
--
Dr Thomas Piggot
University of Southampton, UK.
------------------------------
Message: 5
Date: Wed, 16 May 2012 06:44:54 -0700 (PDT)
From: Shima Arasteh <shima_arasteh2001 at yahoo.com>
Subject: Re: [gmx-users] forcefields for lipids
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <1337175894.2964.YahooMailNeo at web36403.mail.mud.yahoo.com>
Content-Type: text/plain; charset="iso-8859-1"
Thanks for all your suggestions.
Honestly, I want to simulate a protein-membrane system. My chosen membrane is POPC. After the simulation of the system, I'm gonna apply the umbrella sampling on the system to study the ion conduction through the channel composed of this protein.
Before this, I had seen that the ion conduction through the gramicidin A channel in a bilayer were studied using CHARMM. Refer to that article I guess the CHARMM may give me the best? out put. Is this an acceptable choice of a force field?
?
Sincerely,
Shima
________________________________
From: Thomas Piggot <t.piggot at soton.ac.uk>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Wednesday, May 16, 2012 5:55 PM
Subject: Re: [gmx-users] forcefields for lipids
Hi,
In addition to the ones already mentioned (CHARMM, GAFF/AMBER, Berger, OPLS-AA) there are several united-atom GROMOS based lipid forcefields (43A1-S3, 53A6L/54A7, 53A6 Kukol, etc.). The Lipidbook website is a useful place to find lots of lipid parameters in one location:
http://lipidbook.bioch.ox.ac.uk/
The choice of force field will depend upon what you wish to simulate. With PC lipids there are more force fields available compared to other phospholipids, so your choice of lipid may dictate your choice of force field. Additionally some of the available lipid force fields may work well for one type of lipid but not another. Finally if you have a membrane-protein system you also need to consider the combination with an appropriate protein force field.
Cheers
Tom
Peter C. Lai wrote:
> Off the top of my head:
> There are the Berger lipids for the gromos FFs (Justin's tutorial)
> There was a B2 Adrenergic receptor paper that used Amber.
> and of course Martini appears to be everyone's favorite coarse grain FF.
>
> The literature search shall be left as an exercise for the reader.
> (You can even use google to search this mailing list or mirrors of it)
>
> On 2012-05-16 05:59:22AM -0700, Shima Arasteh wrote:
>> Dear gmx users,
>>
>> Which force fields are suggested for lipids? Except CHARMM, any other forcefields?
>> Anybody may suggest me articles in this about?
>>
>>
>> Thanks in advance
>>
>>? Sincerely,
>> Shima
>
>> -- 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
>
>
-- Dr Thomas Piggot
University of Southampton, UK.
-- 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!
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Message: 6
Date: Wed, 16 May 2012 15:25:54 +0100
From: Steven Neumann <s.neumann08 at gmail.com>
Subject: [gmx-users] PMF profile from Umbrella - Plateau
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID:
<CAKZJqQG=OaKzzjenhP8wK+rY--sQmWuJ7n0DkkHjfH25NuazbQ at mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"
Dear Justin,
I pulled my ligad away of 6nm from the protein and obtained beautiful and
smooth curve of PMF using 28 windows. Starting from zero kcal/mol
corresponding to app 0.3 nm then minima and curve increase till my plateau
which starts from app 1 nm - then I have nearly straight line till 6.3 nm.
My question: Can I decrease pulling distance to save time for the future
simualtions with this system in terms of number of water molecules? Shall I
just pull it away of 2-3 nm and I will obtain the same deltaG?
Steven
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