Re: [gmx-users] Regarding using random seed

[Justin Lemkul]

On 3/10/16 3:21 AM, neha chaudhary wrote:

Hello Sir,

Thanks for your help.

I need to clear one more doubt, if I am performing MD simulations with the
mentioned parameter set but using same initial structures then will it
affect the reproducibility of the results.
Actually, I have repeated MD simulations for my protein-ligand complex
three times but I have taken the same initial structure every time using
the same parameters while performing NVT simulations followed by NPT and MD
run (gen-vel = no in npt.mdp and md.mdp file). Is this procedure correct if
I want to testify the reliability of my results.



"Reliability" and "reproducibility" are different things.  Your results are 
reliable if you have (1) a sound physical model, (2) application of appropriate 
algorithms, and (3) sufficient sampling.  Running multiple simulations addresses 
point 3 but not the other two.  Reproducibility means you get the same average 
behavior, so that's related to point 3, but that does not mean that everything 
will be exactly the same (or even that the same .tpr will necessarily generate 
binary identical trajectories; see the GROMACS website for discussion on this 
topic).


-Justin


continuation = no
gen-vel = yes
gen-seed = -1


Best Regards,

*Neha*

Research Scholar,
Centre for Computational Biology and Bioinformatics,
School of Life Sciences,
Central University of Himachal Pradesh,





On Wed, Mar 9, 2016 at 6:36 PM, Tsjerk Wassenaar  wrote:


Right!

T.
On Mar 9, 2016 12:24 PM, "neha chaudhary" 
wrote:


Hi,

So all I have to do is to extract different configurations from my

already

performed MD simulation. Then I have to prepare a new system using that
configuration with the following parameters and rerun the simulations:

continuation = no
gen_vel = yes
gen-seed = -1

Right?


Best Regards,

*Neha*

Research Scholar,
Centre for Computational Biology and Bioinformatics,
School of Life Sciences,
Central University of Himachal Pradesh,





On Wed, Mar 9, 2016 at 4:06 PM, Tsjerk Wassenaar 
wrote:


Hi Neha,

Set

continuation = no
gen_vel = yes

(check http://manual.gromacs.org/online/mdp_opt.html#vel)

Best,

Tsjerk


On Wed, Mar 9, 2016 at 11:16 AM, neha chaudhary <
nehachaudhary...@gmail.com>
wrote:


Thanks Tsjerk for replying,

I want to ask one more question that to start with new velocities,

what

changes I have to make and in which .mdp file?

Best Regards,

*Neha*

Research Scholar,
Centre for Computational Biology and Bioinformatics,
School of Life Sciences,
Central University of Himachal Pradesh,





On Wed, Mar 9, 2016 at 3:37 PM, Tsjerk Wassenaar 
wrote:


Hi Neha,

You can perform a simulation first, and then extract

configurations,

which

you simulate with new starting velocities. Alternatively, you can

generate

a number of different starting structures using elastic-network

modeling,

like with the ElNemo server. Mind to first energy minimize the

resulting,

extrapolated structures, as they may be stretchedhere and there.

Hope it helps,

Tsjerk

On Wed, Mar 9, 2016 at 10:54 AM, neha chaudhary <
nehachaudhary...@gmail.com>
wrote:


Hello there,


Can anyone tell me how can I start my MD simulations with

different

starting structure (random seed) for my protein-ligand complex.

Can I

start

with different sets of coordinates and velocities? If yes, how?


Thanks,

*Neha*
Research Scholar,
Centre for Computational Biology and Bioinformatics,
School of Life Sciences,
Central University of Himachal Pradesh,
--
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Re: [gmx-users] Regarding using random seed

[neha chaudhary]

Hello Sir,

Thanks for your help.

I need to clear one more doubt, if I am performing MD simulations with the
mentioned parameter set but using same initial structures then will it
affect the reproducibility of the results.
Actually, I have repeated MD simulations for my protein-ligand complex
three times but I have taken the same initial structure every time using
the same parameters while performing NVT simulations followed by NPT and MD
run (gen-vel = no in npt.mdp and md.mdp file). Is this procedure correct if
I want to testify the reliability of my results.

continuation = no
gen-vel = yes
gen-seed = -1


Best Regards,

*Neha*

Research Scholar,
Centre for Computational Biology and Bioinformatics,
School of Life Sciences,
Central University of Himachal Pradesh,





On Wed, Mar 9, 2016 at 6:36 PM, Tsjerk Wassenaar  wrote:

> Right!
>
> T.
> On Mar 9, 2016 12:24 PM, "neha chaudhary" 
> wrote:
>
> > Hi,
> >
> > So all I have to do is to extract different configurations from my
> already
> > performed MD simulation. Then I have to prepare a new system using that
> > configuration with the following parameters and rerun the simulations:
> >
> > continuation = no
> > gen_vel = yes
> > gen-seed = -1
> >
> > Right?
> >
> >
> > Best Regards,
> >
> > *Neha*
> >
> > Research Scholar,
> > Centre for Computational Biology and Bioinformatics,
> > School of Life Sciences,
> > Central University of Himachal Pradesh,
> >
> >
> >
> >
> >
> > On Wed, Mar 9, 2016 at 4:06 PM, Tsjerk Wassenaar 
> > wrote:
> >
> > > Hi Neha,
> > >
> > > Set
> > >
> > > continuation = no
> > > gen_vel = yes
> > >
> > > (check http://manual.gromacs.org/online/mdp_opt.html#vel)
> > >
> > > Best,
> > >
> > > Tsjerk
> > >
> > >
> > > On Wed, Mar 9, 2016 at 11:16 AM, neha chaudhary <
> > > nehachaudhary...@gmail.com>
> > > wrote:
> > >
> > > > Thanks Tsjerk for replying,
> > > >
> > > > I want to ask one more question that to start with new velocities,
> what
> > > > changes I have to make and in which .mdp file?
> > > >
> > > > Best Regards,
> > > >
> > > > *Neha*
> > > >
> > > > Research Scholar,
> > > > Centre for Computational Biology and Bioinformatics,
> > > > School of Life Sciences,
> > > > Central University of Himachal Pradesh,
> > > >
> > > >
> > > >
> > > >
> > > >
> > > > On Wed, Mar 9, 2016 at 3:37 PM, Tsjerk Wassenaar 
> > > > wrote:
> > > >
> > > > > Hi Neha,
> > > > >
> > > > > You can perform a simulation first, and then extract
> configurations,
> > > > which
> > > > > you simulate with new starting velocities. Alternatively, you can
> > > > generate
> > > > > a number of different starting structures using elastic-network
> > > modeling,
> > > > > like with the ElNemo server. Mind to first energy minimize the
> > > resulting,
> > > > > extrapolated structures, as they may be stretchedhere and there.
> > > > >
> > > > > Hope it helps,
> > > > >
> > > > > Tsjerk
> > > > >
> > > > > On Wed, Mar 9, 2016 at 10:54 AM, neha chaudhary <
> > > > > nehachaudhary...@gmail.com>
> > > > > wrote:
> > > > >
> > > > > > Hello there,
> > > > > >
> > > > > >
> > > > > > Can anyone tell me how can I start my MD simulations with
> different
> > > > > > starting structure (random seed) for my protein-ligand complex.
> > Can I
> > > > > start
> > > > > > with different sets of coordinates and velocities? If yes, how?
> > > > > >
> > > > > >
> > > > > > Thanks,
> > > > > >
> > > > > > *Neha*
> > > > > > Research Scholar,
> > > > > > Centre for Computational Biology and Bioinformatics,
> > > > > > School of Life Sciences,
> > > > > > Central University of Himachal Pradesh,
> > > > > > --
> > > > > > 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-requ...@gromacs.org.
> > > > > >
> > > > >
> > > > >
> > > > >
> > > > > --
> > > > > Tsjerk A. Wassenaar, Ph.D.
> > > > > --
> > > > > Gromacs Users mailing list
> > > > >
> > > > > * Please search the archive at
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> > > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> > or
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> > > > >
> > > > --
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> > > >
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> > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > > posting!
> > > >
> > > > * Can't post? Read 

Re: [gmx-users] Regarding using random seed

[Tsjerk Wassenaar]

Right!

T.
On Mar 9, 2016 12:24 PM, "neha chaudhary" 
wrote:

> Hi,
>
> So all I have to do is to extract different configurations from my already
> performed MD simulation. Then I have to prepare a new system using that
> configuration with the following parameters and rerun the simulations:
>
> continuation = no
> gen_vel = yes
> gen-seed = -1
>
> Right?
>
>
> Best Regards,
>
> *Neha*
>
> Research Scholar,
> Centre for Computational Biology and Bioinformatics,
> School of Life Sciences,
> Central University of Himachal Pradesh,
>
>
>
>
>
> On Wed, Mar 9, 2016 at 4:06 PM, Tsjerk Wassenaar 
> wrote:
>
> > Hi Neha,
> >
> > Set
> >
> > continuation = no
> > gen_vel = yes
> >
> > (check http://manual.gromacs.org/online/mdp_opt.html#vel)
> >
> > Best,
> >
> > Tsjerk
> >
> >
> > On Wed, Mar 9, 2016 at 11:16 AM, neha chaudhary <
> > nehachaudhary...@gmail.com>
> > wrote:
> >
> > > Thanks Tsjerk for replying,
> > >
> > > I want to ask one more question that to start with new velocities, what
> > > changes I have to make and in which .mdp file?
> > >
> > > Best Regards,
> > >
> > > *Neha*
> > >
> > > Research Scholar,
> > > Centre for Computational Biology and Bioinformatics,
> > > School of Life Sciences,
> > > Central University of Himachal Pradesh,
> > >
> > >
> > >
> > >
> > >
> > > On Wed, Mar 9, 2016 at 3:37 PM, Tsjerk Wassenaar 
> > > wrote:
> > >
> > > > Hi Neha,
> > > >
> > > > You can perform a simulation first, and then extract configurations,
> > > which
> > > > you simulate with new starting velocities. Alternatively, you can
> > > generate
> > > > a number of different starting structures using elastic-network
> > modeling,
> > > > like with the ElNemo server. Mind to first energy minimize the
> > resulting,
> > > > extrapolated structures, as they may be stretchedhere and there.
> > > >
> > > > Hope it helps,
> > > >
> > > > Tsjerk
> > > >
> > > > On Wed, Mar 9, 2016 at 10:54 AM, neha chaudhary <
> > > > nehachaudhary...@gmail.com>
> > > > wrote:
> > > >
> > > > > Hello there,
> > > > >
> > > > >
> > > > > Can anyone tell me how can I start my MD simulations with different
> > > > > starting structure (random seed) for my protein-ligand complex.
> Can I
> > > > start
> > > > > with different sets of coordinates and velocities? If yes, how?
> > > > >
> > > > >
> > > > > Thanks,
> > > > >
> > > > > *Neha*
> > > > > Research Scholar,
> > > > > Centre for Computational Biology and Bioinformatics,
> > > > > School of Life Sciences,
> > > > > Central University of Himachal Pradesh,
> > > > > --
> > > > > 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-requ...@gromacs.org.
> > > > >
> > > >
> > > >
> > > >
> > > > --
> > > > Tsjerk A. Wassenaar, Ph.D.
> > > > --
> > > > 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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> or
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> > > >
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at
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> > > posting!
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> > > send a mail to gmx-users-requ...@gromacs.org.
> > >
> >
> >
> >
> > --
> > Tsjerk A. Wassenaar, Ph.D.
> > --
> > 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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Re: [gmx-users] Regarding using random seed

[neha chaudhary]

Hi,

So all I have to do is to extract different configurations from my already
performed MD simulation. Then I have to prepare a new system using that
configuration with the following parameters and rerun the simulations:

continuation = no
gen_vel = yes
gen-seed = -1

Right?


Best Regards,

*Neha*

Research Scholar,
Centre for Computational Biology and Bioinformatics,
School of Life Sciences,
Central University of Himachal Pradesh,





On Wed, Mar 9, 2016 at 4:06 PM, Tsjerk Wassenaar  wrote:

> Hi Neha,
>
> Set
>
> continuation = no
> gen_vel = yes
>
> (check http://manual.gromacs.org/online/mdp_opt.html#vel)
>
> Best,
>
> Tsjerk
>
>
> On Wed, Mar 9, 2016 at 11:16 AM, neha chaudhary <
> nehachaudhary...@gmail.com>
> wrote:
>
> > Thanks Tsjerk for replying,
> >
> > I want to ask one more question that to start with new velocities, what
> > changes I have to make and in which .mdp file?
> >
> > Best Regards,
> >
> > *Neha*
> >
> > Research Scholar,
> > Centre for Computational Biology and Bioinformatics,
> > School of Life Sciences,
> > Central University of Himachal Pradesh,
> >
> >
> >
> >
> >
> > On Wed, Mar 9, 2016 at 3:37 PM, Tsjerk Wassenaar 
> > wrote:
> >
> > > Hi Neha,
> > >
> > > You can perform a simulation first, and then extract configurations,
> > which
> > > you simulate with new starting velocities. Alternatively, you can
> > generate
> > > a number of different starting structures using elastic-network
> modeling,
> > > like with the ElNemo server. Mind to first energy minimize the
> resulting,
> > > extrapolated structures, as they may be stretchedhere and there.
> > >
> > > Hope it helps,
> > >
> > > Tsjerk
> > >
> > > On Wed, Mar 9, 2016 at 10:54 AM, neha chaudhary <
> > > nehachaudhary...@gmail.com>
> > > wrote:
> > >
> > > > Hello there,
> > > >
> > > >
> > > > Can anyone tell me how can I start my MD simulations with different
> > > > starting structure (random seed) for my protein-ligand complex. Can I
> > > start
> > > > with different sets of coordinates and velocities? If yes, how?
> > > >
> > > >
> > > > Thanks,
> > > >
> > > > *Neha*
> > > > Research Scholar,
> > > > Centre for Computational Biology and Bioinformatics,
> > > > School of Life Sciences,
> > > > Central University of Himachal Pradesh,
> > > > --
> > > > 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-requ...@gromacs.org.
> > > >
> > >
> > >
> > >
> > > --
> > > Tsjerk A. Wassenaar, Ph.D.
> > > --
> > > 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-requ...@gromacs.org.
> > >
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
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> > posting!
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> >
>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
> --
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>
> * Please search the archive at
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Re: [gmx-users] Regarding using random seed

[Tsjerk Wassenaar]

Hi Neha,

Set

continuation = no
gen_vel = yes

(check http://manual.gromacs.org/online/mdp_opt.html#vel)

Best,

Tsjerk


On Wed, Mar 9, 2016 at 11:16 AM, neha chaudhary 
wrote:

> Thanks Tsjerk for replying,
>
> I want to ask one more question that to start with new velocities, what
> changes I have to make and in which .mdp file?
>
> Best Regards,
>
> *Neha*
>
> Research Scholar,
> Centre for Computational Biology and Bioinformatics,
> School of Life Sciences,
> Central University of Himachal Pradesh,
>
>
>
>
>
> On Wed, Mar 9, 2016 at 3:37 PM, Tsjerk Wassenaar 
> wrote:
>
> > Hi Neha,
> >
> > You can perform a simulation first, and then extract configurations,
> which
> > you simulate with new starting velocities. Alternatively, you can
> generate
> > a number of different starting structures using elastic-network modeling,
> > like with the ElNemo server. Mind to first energy minimize the resulting,
> > extrapolated structures, as they may be stretchedhere and there.
> >
> > Hope it helps,
> >
> > Tsjerk
> >
> > On Wed, Mar 9, 2016 at 10:54 AM, neha chaudhary <
> > nehachaudhary...@gmail.com>
> > wrote:
> >
> > > Hello there,
> > >
> > >
> > > Can anyone tell me how can I start my MD simulations with different
> > > starting structure (random seed) for my protein-ligand complex. Can I
> > start
> > > with different sets of coordinates and velocities? If yes, how?
> > >
> > >
> > > Thanks,
> > >
> > > *Neha*
> > > Research Scholar,
> > > Centre for Computational Biology and Bioinformatics,
> > > School of Life Sciences,
> > > Central University of Himachal Pradesh,
> > > --
> > > 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-requ...@gromacs.org.
> > >
> >
> >
> >
> > --
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Re: [gmx-users] Regarding using random seed

[neha chaudhary]

Thanks Tsjerk for replying,

I want to ask one more question that to start with new velocities, what
changes I have to make and in which .mdp file?

Best Regards,

*Neha*

Research Scholar,
Centre for Computational Biology and Bioinformatics,
School of Life Sciences,
Central University of Himachal Pradesh,





On Wed, Mar 9, 2016 at 3:37 PM, Tsjerk Wassenaar  wrote:

> Hi Neha,
>
> You can perform a simulation first, and then extract configurations, which
> you simulate with new starting velocities. Alternatively, you can generate
> a number of different starting structures using elastic-network modeling,
> like with the ElNemo server. Mind to first energy minimize the resulting,
> extrapolated structures, as they may be stretchedhere and there.
>
> Hope it helps,
>
> Tsjerk
>
> On Wed, Mar 9, 2016 at 10:54 AM, neha chaudhary <
> nehachaudhary...@gmail.com>
> wrote:
>
> > Hello there,
> >
> >
> > Can anyone tell me how can I start my MD simulations with different
> > starting structure (random seed) for my protein-ligand complex. Can I
> start
> > with different sets of coordinates and velocities? If yes, how?
> >
> >
> > Thanks,
> >
> > *Neha*
> > Research Scholar,
> > Centre for Computational Biology and Bioinformatics,
> > School of Life Sciences,
> > Central University of Himachal Pradesh,
> > --
> > 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
> >
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> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
> >
>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
> --
> Gromacs Users mailing list
>
> * Please search the archive at
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Re: [gmx-users] Regarding using random seed

[Tsjerk Wassenaar]

Hi Neha,

You can perform a simulation first, and then extract configurations, which
you simulate with new starting velocities. Alternatively, you can generate
a number of different starting structures using elastic-network modeling,
like with the ElNemo server. Mind to first energy minimize the resulting,
extrapolated structures, as they may be stretchedhere and there.

Hope it helps,

Tsjerk

On Wed, Mar 9, 2016 at 10:54 AM, neha chaudhary 
wrote:

> Hello there,
>
>
> Can anyone tell me how can I start my MD simulations with different
> starting structure (random seed) for my protein-ligand complex. Can I start
> with different sets of coordinates and velocities? If yes, how?
>
>
> Thanks,
>
> *Neha*
> Research Scholar,
> Centre for Computational Biology and Bioinformatics,
> School of Life Sciences,
> Central University of Himachal Pradesh,
> --
> 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-requ...@gromacs.org.
>



-- 
Tsjerk A. Wassenaar, Ph.D.
-- 
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[gmx-users] Regarding using random seed

[neha chaudhary]

Hello there,


Can anyone tell me how can I start my MD simulations with different
starting structure (random seed) for my protein-ligand complex. Can I start
with different sets of coordinates and velocities? If yes, how?


Thanks,

*Neha*
Research Scholar,
Centre for Computational Biology and Bioinformatics,
School of Life Sciences,
Central University of Himachal Pradesh,
-- 
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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