[gmx-users] Fixing periodicity effects on trajectory file

Homa rooz ha.roozbahany at gmail.com
Wed Sep 16 07:24:11 CEST 2015 

Dear Justin
​If you asked about verifying docking process​. I should say, I have worked
with single chain protein and the best ranked binding energy was -7.41
kcal/mol by AutoDock 4.2, considering that binding site was located on turn
structure and the edge of protein, seeming unstable. I didn't check the
result by another software.

On Tue, Sep 15, 2015 at 5:29 PM, <
gromacs.org_gmx-users-request at maillist.sys.kth.se> wrote:

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> Today's Topics:
>
>    1. Fixing periodicity effects on trajectory file (Homa rooz)
>    2. Re: Fixing periodicity effects on trajectory file (Justin Lemkul)
>    3. Accelerating data analysis. (Dawid das)
>    4. Re: Accelerating data analysis. (Justin Lemkul)
>    5. Re: Accelerating data analysis. (Erik Marklund)
>    6. Re: Accelerating data analysis. (Dawid das)
>    7. Re: Accelerating data analysis. (Dawid das)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 15 Sep 2015 16:09:15 +0430
> From: Homa rooz <ha.roozbahany at gmail.com>
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: [gmx-users] Fixing periodicity effects on trajectory file
> Message-ID:
>         <
> CACC+7LgC90v1Vb-7+RfRvDhZ4SvK5RY8qQoxTU7WjJH1bsiH+Q at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi there
> I'm working with gromacs for ligand-protein interaction simulation. I have
> run MD for docked complex and now there is a problem with trajectory
> visualization by VMD. The ligand has left binding site circulating around
> the protein.
> I tried to fix the problem by making index and extract the first frame from
> the trajectory to use as  reference and also running "-center", "no jump",
> "no pbc", "-fit rot" but the problem still exists. I'm quite confused.
> Should I execute fixing command in the special order?
> Which group is more preferred to be located at the center,Protein or
> system(non-solvent)?
> I would be grateful if you could help me in this matter.
> --
> Homa Ahmadi
> Shahed University
> Faculty of Basic Sciences
> Alternative email> h.ahmadi at shahed.ac.ir <h.ahmadi at ast.ui.ac.ir>
>
>
> ------------------------------
>
> Message: 2
> Date: Tue, 15 Sep 2015 07:42:37 -0400
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Fixing periodicity effects on trajectory file
> Message-ID: <55F8042D.9060702 at vt.edu>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
>
>
> On 9/15/15 7:39 AM, Homa rooz wrote:
> > Hi there
> > I'm working with gromacs for ligand-protein interaction simulation. I
> have
> > run MD for docked complex and now there is a problem with trajectory
> > visualization by VMD. The ligand has left binding site circulating around
> > the protein.
> > I tried to fix the problem by making index and extract the first frame
> from
> > the trajectory to use as  reference and also running "-center", "no
> jump",
> > "no pbc", "-fit rot" but the problem still exists. I'm quite confused.
> > Should I execute fixing command in the special order?
> > Which group is more preferred to be located at the center,Protein or
> > system(non-solvent)?
>
> If the system is a simple binary protein:ligand complex in water, trjconv
> -center -pbc mol should do it.  Center on the protein, output whatever is
> meaningful to you.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
>
>
> ------------------------------
>
> Message: 3
> Date: Tue, 15 Sep 2015 13:37:45 +0100
> From: Dawid das <addiw7 at googlemail.com>
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: [gmx-users] Accelerating data analysis.
> Message-ID:
>         <
> CAKSLqn7rUvX00gNHFXt-s3pV83R01E1TpJg2cttvRxVudy7N6Q at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Dear Gromacs Experts,
>
> I have an enormous *trr file, which has 1 000 000 points. Now, I know that
> I can modify this file with trjconv, but let's say I do not want to do it,
> but I want to have my 1 000 000 points in *xvg file when I use g_rms for
> instance.
> Is there a way to accelarate it?
>
> Best wishes,
>
> Dawid Grabarek
>
>
> ------------------------------
>
> Message: 4
> Date: Tue, 15 Sep 2015 08:40:33 -0400
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Accelerating data analysis.
> Message-ID: <55F811C1.1040906 at vt.edu>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
>
>
> On 9/15/15 8:37 AM, Dawid das wrote:
> > Dear Gromacs Experts,
> >
> > I have an enormous *trr file, which has 1 000 000 points. Now, I know
> that
> > I can modify this file with trjconv, but let's say I do not want to do
> it,
> > but I want to have my 1 000 000 points in *xvg file when I use g_rms for
> > instance.
> > Is there a way to accelarate it?
> >
>
> Analysis tools (outside of some parts of g_hbond and g_wham) are not
> parallelized, so no, not without modifying the code itself.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> 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: Tue, 15 Sep 2015 12:42:38 +0000
> From: Erik Marklund <erik.marklund at chem.ox.ac.uk>
> To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] Accelerating data analysis.
> Message-ID: <72535074-8285-4E7E-8298-93BD4CBE8EED at chem.ox.ac.uk>
> Content-Type: text/plain; charset="us-ascii"
>
> Dear Dawid,
>
> The best thing I can think of is to analyse different parts of the
> trajectory in parallel, using separate g_rms processes, then concatenating
> the output. Use -b and -e options to limit the analysis to specific
> intervals.
>
> Kind regards,
> Erik
>
> > On 15 Sep 2015, at 13:37, Dawid das <addiw7 at googlemail.com> wrote:
> >
> > Dear Gromacs Experts,
> >
> > I have an enormous *trr file, which has 1 000 000 points. Now, I know
> that
> > I can modify this file with trjconv, but let's say I do not want to do
> it,
> > but I want to have my 1 000 000 points in *xvg file when I use g_rms for
> > instance.
> > Is there a way to accelarate it?
> >
> > Best wishes,
> >
> > Dawid Grabarek
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>
>
>
> ------------------------------
>
> Message: 6
> Date: Tue, 15 Sep 2015 13:45:17 +0100
> From: Dawid das <addiw7 at googlemail.com>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Accelerating data analysis.
> Message-ID:
>         <
> CAKSLqn4LgMRx3uWHQcmMCXnRZvsjWyB5eGYY8b9h6vSKwK1EJA at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Dear All,
>
> Thank you all. Especially for your tip Erik ;).
>
> Dawid
>
> 2015-09-15 13:42 GMT+01:00 Erik Marklund <erik.marklund at chem.ox.ac.uk>:
>
> > Dear Dawid,
> >
> > The best thing I can think of is to analyse different parts of the
> > trajectory in parallel, using separate g_rms processes, then
> concatenating
> > the output. Use -b and -e options to limit the analysis to specific
> > intervals.
> >
> > Kind regards,
> > Erik
> >
> > > On 15 Sep 2015, at 13:37, Dawid das <addiw7 at googlemail.com> wrote:
> > >
> > > Dear Gromacs Experts,
> > >
> > > I have an enormous *trr file, which has 1 000 000 points. Now, I know
> > that
> > > I can modify this file with trjconv, but let's say I do not want to do
> > it,
> > > but I want to have my 1 000 000 points in *xvg file when I use g_rms
> for
> > > instance.
> > > Is there a way to accelarate it?
> > >
> > > Best wishes,
> > >
> > > Dawid Grabarek
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> > >
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> > > * For (un)subscribe requests visit
> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> >
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
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> > send a mail to gmx-users-request at gromacs.org.
> >
>
>
> ------------------------------
>
> Message: 7
> Date: Tue, 15 Sep 2015 13:59:07 +0100
> From: Dawid das <addiw7 at googlemail.com>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Accelerating data analysis.
> Message-ID:
>         <CAKSLqn7C1bWYUS_uS+qbf0b5AAR=
> GwdpaTppBw9rn4HmbhQkBw at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Something is wrong here. I use following command:
>
> g_rms -tu us -b 0.9 -e 1.0 -s npt-md2.tpr -f npt-md2.trr -n index.ndx -o
> rmsd-protein.xvg
>
> and g_rmsd still starts from 0 and it says "Skipping frame..." and it seems
> it will skip all frames (as it would read it) until 0.9 us.
> Is that what I should expect?
>
>
> 2015-09-15 13:45 GMT+01:00 Dawid das <addiw7 at googlemail.com>:
>
> > Dear All,
> >
> > Thank you all. Especially for your tip Erik ;).
> >
> > Dawid
> >
> > 2015-09-15 13:42 GMT+01:00 Erik Marklund <erik.marklund at chem.ox.ac.uk>:
> >
> >> Dear Dawid,
> >>
> >> The best thing I can think of is to analyse different parts of the
> >> trajectory in parallel, using separate g_rms processes, then
> concatenating
> >> the output. Use -b and -e options to limit the analysis to specific
> >> intervals.
> >>
> >> Kind regards,
> >> Erik
> >>
> >> > On 15 Sep 2015, at 13:37, Dawid das <addiw7 at googlemail.com> wrote:
> >> >
> >> > Dear Gromacs Experts,
> >> >
> >> > I have an enormous *trr file, which has 1 000 000 points. Now, I know
> >> that
> >> > I can modify this file with trjconv, but let's say I do not want to do
> >> it,
> >> > but I want to have my 1 000 000 points in *xvg file when I use g_rms
> for
> >> > instance.
> >> > Is there a way to accelarate it?
> >> >
> >> > Best wishes,
> >> >
> >> > Dawid Grabarek
> >> > --
> >> > Gromacs Users mailing list
> >> >
> >> > * Please search the archive at
> >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> >> posting!
> >> >
> >> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >> >
> >> > * For (un)subscribe requests visit
> >> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> >> send a mail to gmx-users-request at gromacs.org.
> >>
> >> --
> >> Gromacs Users mailing list
> >>
> >> * Please search the archive at
> >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> >> posting!
> >>
> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>
> >> * For (un)subscribe requests visit
> >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> >> send a mail to gmx-users-request at gromacs.org.
> >>
> >
> >
>
>
> ------------------------------
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
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> End of gromacs.org_gmx-users Digest, Vol 137, Issue 82
> ******************************************************
>



-- 
Homa Ahmadi
Shahed University
Faculty of Basic Sciences
Alternative email> h.ahmadi at shahed.ac.ir <h.ahmadi at ast.ui.ac.ir>

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