[gmx-users] RE: Stopping protein jumping inside box?
라지브간디
rajiv at kaist.ac.kr
Thu Feb 14 06:13:03 CET 2013
Dear gmx,
I've used -pbc nojump options but still the protein goes all around the box within 4ns. Any specific command to avoid this ? It's a myoglobin protein!
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Today's Topics:
1. Stopping protein jumping inside box (?????)
2. Re: Stopping protein jumping inside box (Naga Sundar)
3. Re: Stopping protein jumping inside box (Justin Lemkul)
4. RE: on the ussage of SD1 integrator (Berk Hess)
5. Chandler autcorrelation function fitting (KARAKAS Esra)
6. Bond potential of atom groups (Steven Neumann)
7. Join my network on LinkedIn (Gideon Lapidoth via LinkedIn)
8. GROMOS54A8 parameters in GROMACS format (ABEL Stephane 175950)
9. Re: different springs - WHAM (Steven Neumann)
----------------------------------------------------------------------
Message: 1
Date: Wed, 13 Feb 2013 22:29:05 +0900 (KST)
From: ????? <rajiv at kaist.ac.kr>
Subject: [gmx-users] Stopping protein jumping inside box
To: gmx-users at gromacs.org
Message-ID: <511b98243fa7_ at _imoxion.com>
Content-Type: text/plain; charset="utf-8"
Dear gmx users,
I need to stop my protein jumping inside box. I have used -pbc mol -ur compact -center command too but still the protein gets moving from one place to other.
Could you please suggest me how to make the protein to stop in one place ? Moreover, its protein with their ligand.
Thnx.
------------------------------
Message: 2
Date: Wed, 13 Feb 2013 05:47:07 -0800
From: Naga Sundar <naga25sundar at gmail.com>
Subject: Re: [gmx-users] Stopping protein jumping inside box
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID:
<CALobX4n_6hUoJhV-AEcjGj9UctvivV2H5U-+iZyVizmr0ECv6Q at mail.gmail.com>
Content-Type: text/plain; charset=EUC-KR
Hi
Plz try -pbc nojump option...It may work
On Wed, Feb 13, 2013 at 5:29 AM, ���������� <rajiv at kaist.ac.kr> wrote:
> Dear gmx users,
>
>
> I need to stop my protein jumping inside box. I have used -pbc mol -ur
> compact -center command too but still the protein gets moving from one
> place to other.
>
>
> Could you please suggest me how to make the protein to stop in one place ?
> Moreover, its protein with their ligand.
>
>
>
>
> Thnx.
>
>
>
> --
> gmx-users mailing list gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at
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>
--
Regards
N.NagaSundaram
------------------------------
Message: 3
Date: Wed, 13 Feb 2013 08:50:04 -0500
From: Justin Lemkul <jalemkul at vt.edu>
Subject: Re: [gmx-users] Stopping protein jumping inside box
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <511B9A0C.9 at vt.edu>
Content-Type: text/plain; charset=UTF-8; format=flowed
On 2/13/13 8:47 AM, Naga Sundar wrote:
> Hi
> Plz try -pbc nojump option...It may work
>
Several iterations of trjconv are often needed to achieve the desired
representation. Indeed, the first step to removing jumps should be -pbc
nojump...which removes jumps ;)
-Justin
> On Wed, Feb 13, 2013 at 5:29 AM, ��������������� <rajiv at kaist.ac.kr> wrote:
>
>> Dear gmx users,
>>
>>
>> I need to stop my protein jumping inside box. I have used -pbc mol -ur
>> compact -center command too but still the protein gets moving from one
>> place to other.
>>
>>
>> Could you please suggest me how to make the protein to stop in one place ?
>> Moreover, its protein with their ligand.
>>
>>
>>
>>
>> Thnx.
>>
>>
>>
>> --
>> 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.
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: Wed, 13 Feb 2013 15:57:34 +0100
From: Berk Hess <gmx3 at hotmail.com>
Subject: RE: [gmx-users] on the ussage of SD1 integrator
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <DUB124-W136490404914302A83F9B68E080 at phx.gbl>
Content-Type: text/plain; charset="iso-8859-1"
Hi,
With tau_t=2 the sd1 integrator should be ok.
But in 4.6.1, which will be released this week, the performance issues with the sd integrator are fixed.
Cheers,
Berk
> Date: Wed, 13 Feb 2013 09:19:46 +0300
> From: jmsstarlight at gmail.com
> To: gmx-users at gromacs.org
> Subject: [gmx-users] on the ussage of SD1 integrator
>
> Dear Gromacs users!
>
>
> Commonly I'm using langevin's dynamics for thermostat modelling in my
> simulations of the membrane proteins
> (sd integrator without t_coupl with tau_t=2.0)
>
> Recently I've found that with sd1 integrator I can obtain better
> performance ( up to 50% in comparison to sd integrator). Could I use
> that integrator for modelling of stochastic thermostat with the same
> tau_t which I've used with SD ?
> Also during ussage of that thermostat I obtain notions from grommp like
>
> NOTE 4 [file ./mdps_cuda/md_sd.mdp]:
> With constraints integrator sd1 is less accurate, consider using sd
> instead
>
> What should I do to reduce such degree of inacuracy of SD1?
>
> Thanks for help,
>
> James
> --
> 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: 5
Date: Wed, 13 Feb 2013 15:36:48 +0000
From: KARAKAS Esra <Esra.Karakas at cea.fr>
Subject: [gmx-users] Chandler autcorrelation function fitting
To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
Message-ID:
<981823ADF8938344AE9DE8F0922F6494AD408E at E-EXDAGE-A0.extra.cea.fr>
Content-Type: text/plain; charset="iso-8859-1"
Dear gromacs users,
I would like to compute the transition time gauche-trans for dihedral angles.
For that, I used this command :
g_angle_mpi -f myfile.xtc -n dihedral.ndx -b 25000 -e 30000 -type dihedral -chandler -avercorr -oc myoutput.xvg
I have dihedral autocorrelation function C(t) but I can't manage to fit this curve with a function.
Anybody know how this autocorrelation function is computed and with what kind of function I can fit it ?
Thanks for help,
Esra
------------------------------
Message: 6
Date: Wed, 13 Feb 2013 16:07:53 +0000
From: Steven Neumann <s.neumann08 at gmail.com>
Subject: [gmx-users] Bond potential of atom groups
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID:
<CAKZJqQEztzuGqm0t4=f37v+W-jioiRE0pz1tvDpJ6cV7CyGLOA at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1
Dear Gmx Users,
I want to create coarse grained model. I need bond constant and
equilibrium distance according to the equation
V(r) =K (R - Req)^2
I wish to extract bonded potential between beads made out 3 atoms. I
need Req and K. Equilibrium distance is straight forward - g_dist
between COM or COG with index file conatining those 3 atoms. To match
force constant K I need to extract bonded potential and try to fit to
my parabolic curve.
My question:
How can I get bonded potential between beads of 3 atoms from AA
simulation? Do I have to specify energy groups (energgrps) before the
run in my mdp and then use g_energy?
Thank you
Steven
------------------------------
Message: 7
Date: Wed, 13 Feb 2013 16:36:35 +0000 (UTC)
From: Gideon Lapidoth via LinkedIn <member at linkedin.com>
Subject: [gmx-users] Join my network on LinkedIn
To: "Chinmay D." <gmx-users at gromacs.org>
Message-ID:
<1132639804.8784666.1360773395306.JavaMail.app at ela4-app2322.prod>
Content-Type: text/plain; charset=UTF-8
LinkedIn
------------
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- Gideon
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------------------------------
Message: 8
Date: Wed, 13 Feb 2013 21:25:33 +0000
From: ABEL Stephane 175950 <Stephane.ABEL at cea.fr>
Subject: [gmx-users] GROMOS54A8 parameters in GROMACS format
To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
Message-ID:
<3E39B768BB199548AB18F7289E7534AF02D60FD9 at EXDAG0-B0.intra.cea.fr>
Content-Type: text/plain; charset="utf-8"
Hello all,
Does somebody know where i can find the latest GROMOS force field (i.e. GROMOS54A8) described in [1] in the GROMACS format (gromos54a7.ff) ?
[1] Reif et al. J. Chem. Theory Comput. 2013, 9, 1247���1264 doi: http://pubs.acs.org/doi/citedby/10.1021/ct300156h
Thank you
Stephane
------------------------------
Message: 9
Date: Wed, 13 Feb 2013 22:23:41 +0000
From: Steven Neumann <s.neumann08 at gmail.com>
Subject: Re: [gmx-users] different springs - WHAM
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID:
<CAKZJqQHOYd21hG003DhUuFBtdZSaci8UhF78_Top79Yz7ya_Nw at mail.gmail.com>
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On Tue, Feb 12, 2013 at 5:01 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 2/12/13 9:57 AM, Steven Neumann wrote:
>>
>> On Tue, Feb 12, 2013 at 2:53 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>>
>>>
>>>
>>> On 2/12/13 9:40 AM, Steven Neumann wrote:
>>>>
>>>>
>>>> Dear Gmx Users,
>>>>
>>>> I know it is possible to combine windows with different spring
>>>> constants into the one PMF curve using g_wham.
>>>>
>>>> Do I have to somehow tell g_wham that one or two windows have
>>>> different spring constants?
>>>>
>>>
>>> No, they are read from the .tpr files.
>>>
>>>
>>>> For instance - I got the better histogram overlap with lower force
>>>> constant in one window. When I replace this window into the window
>>>> with the sring constant like all windwos (worse overlap) both PMF
>>>> curves differ app. 2kcal/mol which is around 30% of the overall
>>>> deltaG.
>>>>
>>>> Is there any error I should inroduce when one window differ in terms of
>>>> k1?
>>>>
>>>
>>> What does g_wham's error analysis suggest?
>>>
>>> -Justin
>>
>>
>> In both PMF error estimate with bayesian bootstraping is app. 0.2 kcal/mol
>>
>
> Seems like a good result, so what's the problem?
>
> -Justin
That the better overlap of histograms produce worse deltaG comparing
to experiment. With all the same spring constants I get the
experimental value of deltaG but there is a poor overlap. There must
be (somehow) a correction added to deltaG when introdcuing windows
with different spring constants.
Steven
>
>
> --
> ========================================
>
> 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
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