[gmx-users] quasi-harmonic entropy calculation

[Nivedita Rai]

Hello @all,

Myself Nivedita Rai doing Ph.D. in Bioinformatics from
Pondicherry University (India). I need the correct script to calculate the
entropy. If possible kindly sent me the script.





-- 
Thanks and regards


Nivedita Rai
PhD in Bioinformatics
Centre for Bioinformatics
Pondicherry University, Pondicherry (605014), INDIA
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[gmx-users] Fwd: umbrella sampling

[Nivedita Rai]

-- Forwarded message --
From: Nivedita Rai <bioinfonive...@gmail.com>
Date: Fri, Sep 8, 2017 at 9:39 PM
Subject: umbrella sampling
To: gromacs.org_gmx-users@maillist.sys.kth.se


Dear gromacs developers,

I am trying to implement umbrella sampling in my work but instead of
distance pulling i want to do rotational pull with the gap of 10 degree. I
went through your tutorial and many articles but im unable to find  how to
implement rotational pull in .mdp file. will you please guide me or send me
any article which i can refer for my objective.


-- 
Thanks and regards


Nivedita Rai
PhD in Bioinformatics
Centre for Bioinformatics
Pondicherry University, Pondicherry (605014), INDIA




-- 
Thanks and regards


Nivedita Rai
PhD in Bioinformatics
Centre for Bioinformatics
Pondicherry University, Pondicherry (605014), INDIA
-- 
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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[gmx-users] umbrella sampling

[Nivedita Rai]

Dear gromacs developers,

I am trying to implement umbrella sampling in my work but instead of
distance pulling i want to do rotational pull with the gap of 10 degree. I
went through your tutorial and many articles but im unable to find  how to
implement rotational pull in .mdp file. will you please guide me or send me
any article which i can refer for my objective.


-- 
Thanks and regards


Nivedita Rai
PhD in Bioinformatics
Centre for Bioinformatics
Pondicherry University, Pondicherry (605014), INDIA
-- 
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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[gmx-users] Fwd: protein-ligand complex simulation

[Nivedita Rai]

Dear Gromacs User,

I am running *protein ligand complex* simulation by
following the Beven lab tutorial. while production run im getting two notes
such as:

*NOTE 1* [file topol.top]:
  The largest charge group contains 11 atoms.
  Since atoms only see each other when the centers of geometry of the charge
  groups they belong to are within the cut-off distance, too large charge
  groups can lead to serious cut-off artifacts.
  For efficiency and accuracy, charge group should consist of a few atoms.
  For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc.

Number of degrees of freedom in T-Coupling group Protein_UNK is 8298.87
Number of degrees of freedom in T-Coupling group Water_and_ions is 180606.12
Largest charge group radii for Van der Waals: 0.267, 0.265 nm
Largest charge group radii for Coulomb:   0.267, 0.265 nm
Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 84x84x84, spacing 0.118 0.118 0.118
Estimate for the relative computational load of the PME mesh part: 0.32

NOTE 2 [file md.mdp]:
  This run will generate roughly 5681 Mb of data

Is *note1* will create any trouble? if yes then how to rectify it?

I have already posted this question twice. hope this time I will get the
reply.
-- 
Thanks and regards


Nivedita Rai
PhD in Bioinformatics
-- 
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* Please search the archive at 
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[gmx-users] Protein-ligand complex simulation

[Nivedita Rai]

Dear Gromacs User,

I am running *protein ligand complex* simulation by
following the Beven lab tutorial. while production run im getting two notes
such as:

NOTE 1 [file topol.top]:
  The largest charge group contains 11 atoms.
  Since atoms only see each other when the centers of geometry of the charge
  groups they belong to are within the cut-off distance, too large charge
  groups can lead to serious cut-off artifacts.
  For efficiency and accuracy, charge group should consist of a few atoms.
  For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc.

Number of degrees of freedom in T-Coupling group Protein_UNK is 8298.87
Number of degrees of freedom in T-Coupling group Water_and_ions is 180606.12
Largest charge group radii for Van der Waals: 0.267, 0.265 nm
Largest charge group radii for Coulomb:   0.267, 0.265 nm
Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 84x84x84, spacing 0.118 0.118 0.118
Estimate for the relative computational load of the PME mesh part: 0.32

NOTE 2 [file md.mdp]:
  This run will generate roughly 5681 Mb of data

Is *note1* will create any trouble? if yes then how to rectify it?

-- 
Thanks and regards


Nivedita Rai
PhD in Bioinformatics
Centre for Bioinformatics
Pondicherry University, Pondicherry (605014), INDIA
-- 
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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[gmx-users] Protein-complex simulation

[Nivedita Rai]

Dear gromacs User,
I am running *protein ligand complex* simulation by
following the Beven lab tutorial. while production run im getting two notes
such as:

NOTE 1 [file topol.top]:
  The largest charge group contains 11 atoms.
  Since atoms only see each other when the centers of geometry of the charge
  groups they belong to are within the cut-off distance, too large charge
  groups can lead to serious cut-off artifacts.
  For efficiency and accuracy, charge group should consist of a few atoms.
  For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc.

Number of degrees of freedom in T-Coupling group Protein_UNK is 8298.87
Number of degrees of freedom in T-Coupling group Water_and_ions is 180606.12
Largest charge group radii for Van der Waals: 0.267, 0.265 nm
Largest charge group radii for Coulomb:   0.267, 0.265 nm
Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 84x84x84, spacing 0.118 0.118 0.118
Estimate for the relative computational load of the PME mesh part: 0.32

NOTE 2 [file md.mdp]:
  This run will generate roughly 5681 Mb of data

Is *note1* will create any trouble? if yes then how to rectify it?


-- 
Thanks and regards


Nivedita Rai
PhD in Bioinformatics
Centre for Bioinformatics
Pondicherry University, Pondicherry (605014), INDIA
-- 
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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Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 153, Issue 12

[Nivedita Rai]

Dear User,
while production run im getting two notes such as:

NOTE 1 [file topol.top]:
  The largest charge group contains 11 atoms.
  Since atoms only see each other when the centers of geometry of the charge
  groups they belong to are within the cut-off distance, too large charge
  groups can lead to serious cut-off artifacts.
  For efficiency and accuracy, charge group should consist of a few atoms.
  For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc.

Number of degrees of freedom in T-Coupling group Protein_UNK is 8298.87
Number of degrees of freedom in T-Coupling group Water_and_ions is 180606.12
Largest charge group radii for Van der Waals: 0.267, 0.265 nm
Largest charge group radii for Coulomb:   0.267, 0.265 nm
Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 84x84x84, spacing 0.118 0.118 0.118
Estimate for the relative computational load of the PME mesh part: 0.32

NOTE 2 [file md.mdp]:
  This run will generate roughly 5681 Mb of data

Is *note1* will create any trouble? if yes then how to rectify it?


On Thu, Jan 5, 2017 at 4:30 PM, <
gromacs.org_gmx-users-requ...@maillist.sys.kth.se> wrote:

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> Today's Topics:
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>1. Regression test error in gromacs 5.1.4 installation
>   (Abhisheak Sharma)
>2. Index file group selection and gmx covar error (Aditya Padhi)
>
>
> --
>
> Message: 1
> Date: Thu, 5 Jan 2017 13:01:57 +0530
> From: Abhisheak Sharma 
> To: gromacs.org_gmx-users@maillist.sys.kth.se
> Subject: [gmx-users] Regression test error in gromacs 5.1.4
> installation
> Message-ID:
>  gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hello,
>
> I am trying to install gromacs 5.1.4 and getting following error of
> regression test fail.
>
> Downloading: http://gerrit.gromacs.org/download/regressiontests-5.1.
> 4.tar.gz
> -- [download 100% complete]
> CMake Error at tests/CMakeLists.txt:65 (message):
>   Download of regressiontests failed.  Expected MD5 of
>   8902358ab19343f17997d1bf85f8e69c but download has
>   3a78f965540a904c4cc1dcab1f7e0edb
>
>
> -- Configuring incomplete, errors occurred!
> See also "/home/abhishek/gromacs/gromacs-5.1.4/build/
> CMakeFiles/CMakeOutput.log".
> See also "/home/abhishek/gromacs/gromacs-5.1.4/build/
> CMakeFiles/CMakeError.log".
>
>
>
> I have tried to download regression test file from the web (
> ftp://ftp.gromacs.org/regressiontests/regressiontests-5.1.4.tar.gz) but
> this link is not working. Kindly help me to solve this issue.
>
> Thanks
>
> Abhishek
>
>
> --
>
> Message: 2
> Date: Thu, 5 Jan 2017 17:40:44 +0900
> From: Aditya Padhi 
> To: gmx-us...@gromacs.org
> Subject: [gmx-users] Index file group selection and gmx covar error
> Message-ID:
>