[gmx-users] Regarding protocol of g_lie module

[neha chaudhary]

Dear users,

I want to calculate linear interaction energy for my protein-ligand complex
using g_lie module in Gromacs. I have ran two different simulations of
ligand, one with protein and other with water. But I am getting same values
for GBind while using g_lie for both simulations.

Can anyone help me about the exact usage protocol of g_lie?

Thanks
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[gmx-users] g_mmpbsa compilation error

[neha chaudhary]

Hi,

I am trying to compile g_mmpbsa with APBS for gromacs-5.1.2. APBS and
gromacs installed properly but during cmake for g_mmpbsa I am facing the
following error:

-- Found z library: /usr/lib/x86_64-linux-gnu/libz.so
CMake Error at cmake/FindGROMACS.cmake:203 (list):
  list index: 2 out of range (-2, 1)
Call Stack (most recent call first):
  src/CMakeLists.txt:62 (find_package)


-- Found Gromacs include directory: /usr/local/gromacs/include
-- Configuring incomplete, errors occurred!

Can anyone help me with this?


Best Regards,

Neha
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Re: [gmx-users] Fwd: Segmentation fault (core dumped) in g_mmpbsa

[neha chaudhary]

Hi,

I tried to compile g_mmpbsa with APBS but no success. I am facing the
following error while cmake:

-- Found z library: /usr/lib/x86_64-linux-gnu/libz.so
CMake Error at cmake/FindGROMACS.cmake:203 (list):
  list index: 2 out of range (-2, 1)
Call Stack (most recent call first):
  src/CMakeLists.txt:62 (find_package)


-- Found Gromacs include directory: /usr/local/gromacs/include
-- Configuring incomplete, errors occurred!

Please help.

Thanks.

*Neha*




On Wed, Aug 30, 2017 at 10:42 AM, neha chaudhary <nehachaudhary...@gmail.com
> wrote:

> Hi,
>
> I will download and install APBS and try again.
>
> I have already tried pre-compiled version of g_mmpbsa from the link you
> suggested.
>
> Thanks
>
> Best Regards,
>
> *Neha*
>
> Research Scholar,
> Centre for Computational Biology and Bioinformatics,
> School of Life Sciences,
> Central University of Himachal Pradesh,
>
>
>
>
>
> On Wed, Aug 30, 2017 at 10:38 AM, Nikhil Maroli <scinik...@gmail.com>
> wrote:
>
>> Hell,
>>
>> Download APBS and install it then use the binary package of g_mmpbsa. or
>> see here:
>>
>> Pre-compiled executable program
>>
>> Pre-compiled program does not require any external library or GROMACS and
>> APBS package. These programs are standalone and without any dependency.
>> Download, extract and use it.
>>
>>
>> http://rashmikumari.github.io/g_mmpbsa/Download-and-Installation.html
>> --
>> 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.
>>
>
>
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Re: [gmx-users] Fwd: Segmentation fault (core dumped) in g_mmpbsa

[neha chaudhary]

Hi,

I will download and install APBS and try again.

I have already tried pre-compiled version of g_mmpbsa from the link you
suggested.

Thanks

Best Regards,

*Neha*

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





On Wed, Aug 30, 2017 at 10:38 AM, Nikhil Maroli  wrote:

> Hell,
>
> Download APBS and install it then use the binary package of g_mmpbsa. or
> see here:
>
> Pre-compiled executable program
>
> Pre-compiled program does not require any external library or GROMACS and
> APBS package. These programs are standalone and without any dependency.
> Download, extract and use it.
>
>
> http://rashmikumari.github.io/g_mmpbsa/Download-and-Installation.html
> --
> 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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>
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Re: [gmx-users] Fwd: Segmentation fault (core dumped) in g_mmpbsa

[neha chaudhary]

Hello,

I have not installed APBS. I have compiled g_mmpbsa without APBS. Should I
compile it with APBS?

Best Regards,

*Neha*

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





On Wed, Aug 30, 2017 at 10:23 AM, Nikhil Maroli  wrote:

> Hi,
>
> The segmentation fault error during polar energy calculations is due to
> APBS. I don't know whether you installed it properly or not.
> --
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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 <tsje...@gmail.com> wrote:

> Right!
>
> T.
> On Mar 9, 2016 12:24 PM, "neha chaudhary" <nehachaudhary...@gmail.com>
> 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 <tsje...@gmail.com>
> > 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 <tsje...@gmail.com>
> > > > 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 

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 <tsje...@gmail.com> 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 <tsje...@gmail.com>
> > 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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> > >
> > --
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>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
> --
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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 <tsje...@gmail.com> 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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[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

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[gmx-users] Regarding groups making by make_ndx

[neha chaudhary]

Hello Sir,

I want to make a new group that contain 2-3 amino acid residues present in
protein. But when I am running nvt simulation with this new group error
message like multiple t-coupling groups in (1 and 3). So, I am using
splitres option in make_ndx module of gromacs to separate number of
residues in protein. Is there any way to combine these separated residues
to make a new group .

Best Regards,

*Neha*

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