[gmx-users] RE: Stopping protein jumping inside box?

Mark Abraham mark.j.abraham at gmail.com
Fri Feb 15 09:16:55 CET 2013 

On Thu, Feb 14, 2013 at 6:13 AM, 라지브간디 <rajiv at kaist.ac.kr> wrote:

> 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!
>

The usual approach is here:
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions

Mark


> --------------------- orig.Message ---------------------
> From : gmx-users-request at gromacs.org
> To : gmx-users at gromacs.org
> Sent date : 2013-02-14 07:24
> Subject : gmx-users Digest, Vol 106, Issue 69
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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
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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
> ------------
>
>
>
>
>     Gideon Lapidoth requested to add you as a connection on LinkedIn:
>
>
> ------------------------------------------
>
> Chinmay,
>
> I'd like to add you to my professional network on LinkedIn.
>
> - Gideon
>
> Accept invitation from Gideon Lapidoth
>
> http://www.linkedin.com/e/-85v1n9-hd4pcfob-2u/Xl9gjr6GAOlB4vIjeR9gqTUPRTlBoITTu0/blk/I446675742_16/0UcDpKqiRzolZKqiRybmRSrCBvrmRLoORIrmkZt5YCpnlOt3RApnhMpmdzgmhxrSNBszYSclYOd3sRdPoSd3h9bQtDtD9jbmJfbP4PejkNdzwQczcLrCBxbOYWrSlI/eml-comm_invm-b-in_ac-inv28/?hs=false&tok=3qxljZfqg445E1
>
> View profile of Gideon Lapidoth
>
> http://www.linkedin.com/e/-85v1n9-hd4pcfob-2u/rso/124852802/3yE9/name/15686615_I446675742_16/?hs=false&tok=0-QNCQqiI445E1
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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>
> Content-Type: text/plain; charset=ISO-8859-1
>
> 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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> > interface or send it to gmx-users-request at gromacs.org.
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>
> ------------------------------
>
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> End of gmx-users Digest, Vol 106, Issue 69
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>
>
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