[gmx-users] How to fix the ends of the protein?

[Seera Suryanarayana]

Dear Gromacs users,

I would like to simulate the topological domain of one protein. For that I
need to fix the ends of the simulated protein. How do one can
fix(constraint) the ends of the protein? Kindly help me how to do this
fixation?

Surya
Graduate student
India.
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Re: [gmx-users] DPPC-DOTAP Mixed Lipid Bilayer

[Tsjerk Wassenaar]

Hi Nidhin,

Insane allows you to build lipids from the command line. Alternatively,
it's pretty easy to add DOTAP to insane, using the templates inside. If you
feel you need a hand with that, let me know.

Cheers,

Tsjerk
On Jun 7, 2016 12:21 AM, "Nidhin Thomas" 
wrote:

> Hi GROMACS Users,
>
> I would like to create a mixed bilayer of DPPC and DOTAP lipids for
> research. I usually use charm-gui or insane.py to create a mixed bilayer.
> But I could not find DOTAP listed in either of these lists. When I searched
> online, I got a mixed bilayer system for DMPC & DPPC lipids and the
> parameter file for DOTAP lipid from
> http://www.softsimu.net/downloads.shtml.
>
> My objective is to create mixed lipid bilayer system with various
> percentage of DOTAP lipids. In addition, I have to create a bilayer with
> one DOTAP in each layer and remaining DPPC lipids. Can anyone please guide
> me to create these lipid bilayers? It would be great if someone could
> explain, how to create these mixed bilayers from scratch.
>
> Thanks a lot everyone!,
>
> Nidhin Thomas
> University of Houston
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Re: [gmx-users] Non-bonded energy

[ABANTIKA PAL]

Hi,

So, for calculating non-bonded energy, we have to consider all pair of atoms of 
the protein which are separated by a distance less than the cutoff distance. 
Please correct me if I am wrong.

- Original Message -
From: "Justin Lemkul" 
To: gmx-us...@gromacs.org
Sent: Tuesday, June 7, 2016 6:50:32 AM
Subject: Re: [gmx-users] Non-bonded energy



On 6/6/16 9:00 AM, ABANTIKA PAL wrote:
> Hi,
>
> I want to know which atoms are to be considered while calculating non-bonded 
> energy of a protein. Whether it is all pair atom or there is a particular 
> criteria while selecting the atoms.
>

The nonbonded energy of a protein would imply that any interactions within the 
defined cutoffs would be included.  Of course, such a quantity is not 
physically 
meaningful, but that's how it's calculated.

-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

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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[gmx-users] cannot output all the structures of one cluster

[Zhenyu Meng]

Dear GMX users,
I want to output all the structures of certain cluster using g_cluster, and
the following is my command:
g_cluster -f md5_mol.xtc -s md5.tpr -n index.ndx -o md5.xpm -g
md5_cluster.log -cutoff 0.12 -cl cluster1.gro -wcl 1 -nst 30
While it seems gromacs cannot generate all the structures. Instead, in
cluster1.gro there're only several central structures.
The .log file is like this:
Writing middle structure for each cluster to cluster1.gro
Writing all structures for the first 1 clusters with more than 30
structures to cluster1.gro%01d.gro
But I cannot find cluster1.gro%01d.gro in my directory.
Is there anyone knowing what's going on?
Your help will be highly appreciated!

-- 
Sincerely,
Mr. Meng Zhenyu
Division of Chemistry and Biological Chemistry
School of Physical and Mathematical Sciences
Nanyang Technological University
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Re: [gmx-users] Position restrain of of different chain in fibril structure

[Md. Imrul Reza Shishir]

Dear all
good day.

https://drive.google.com/open?id=0B9FUC_dv9IRoTUdHZENEN1FaOHc

In the google drive file i attached all the file with forcefield file. I
only deleted the nvt.trr file. As this file size very big.

In this run i only use 7 chain of cellulose. to small the calculation step.

Still after the energy minimization. When i run the nvt.mdp then the fibril
structure broken. All chain aligned one by one.

Best regards

Md Imrul Reza Shishir


On Tue, Jun 7, 2016 at 10:19 AM, Justin Lemkul  wrote:

>
>
> On 6/6/16 9:13 PM, Md. Imrul Reza Shishir wrote:
>
>> Dear all
>> I have a structure file of cellulose nano fibril of 36 chain (each have 40
>> residue). I want to simulate it as a single compound. I try to run the
>> simulation with OPLS-AA force field. After energy minimization when i run
>> the equilibrium step then the fibril structure broken and all the chain
>> aligned in a single chain like structure. I want to restrain the position
>> of chain in there original sheet like structure. But I am  not able to
>> define.
>>
>> In the dropbox i attached my simulation structure image file. Initially,
>> it
>> was 7 sheet of 36 cellulose chain (each chain 40 residues). I check the
>> structure (gro file) every stage in VMD after new box creation, solvating,
>> energy minimization. The initial structure is not broken. But after
>> equilibrium stage when I run nvt.mpd it will break it initial stage. And
>> all 36 chain aligned like output structure.
>>
>> *gmx_mpi pdb2gmx -f (filename).pdb -o (filename).gro -water spce -missing*
>>
>> *gmx_mpi editconf -f test_fibril_processed.gro -o
>> test_fibril_newbox.gro -c -d 1.0 -bt cubic *(This box set-up command)
>>
>> I also attached nvt.mdp, npt.mdp and md.mdp file. This simulation is
>> trial run for long time simulation. How should i restrain the position
>> of my structure.
>>
>>
>> In the dropbox link i attached nvt.mdp, npt.mdp, md.mdp and also Input
>> and output structure image in vmd.
>>
>> https://www.dropbox.com/sh/skkskzp1pruf227/AADI2a7TG6pzadFzIEE8094na?dl=0
>>
>> Thank you very much.
>>
>>
> Please upload the actual coordinate files and any relevant topologies.  I
> don't see how setting up that structure in a cubic box would lead to such a
> structure.
>
> -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
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
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>



-- 
*Md Imrul Reza Shishir*
Master Student
*Inha University*
*CRC for NanoCellulose Future Composites*
36 Getbeol-ro, Yeonsu-gu
Incheon 21999
South Korea
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Re: [gmx-users] Non-bonded energy

[Justin Lemkul]

On 6/6/16 9:00 AM, ABANTIKA PAL wrote:

Hi,

I want to know which atoms are to be considered while calculating non-bonded 
energy of a protein. Whether it is all pair atom or there is a particular 
criteria while selecting the atoms.



The nonbonded energy of a protein would imply that any interactions within the 
defined cutoffs would be included.  Of course, such a quantity is not physically 
meaningful, but that's how it's calculated.


-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

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] Position restrain of of different chain in fibril structure

[Justin Lemkul]

On 6/6/16 9:13 PM, Md. Imrul Reza Shishir wrote:

Dear all
I have a structure file of cellulose nano fibril of 36 chain (each have 40
residue). I want to simulate it as a single compound. I try to run the
simulation with OPLS-AA force field. After energy minimization when i run
the equilibrium step then the fibril structure broken and all the chain
aligned in a single chain like structure. I want to restrain the position
of chain in there original sheet like structure. But I am  not able to
define.

In the dropbox i attached my simulation structure image file. Initially, it
was 7 sheet of 36 cellulose chain (each chain 40 residues). I check the
structure (gro file) every stage in VMD after new box creation, solvating,
energy minimization. The initial structure is not broken. But after
equilibrium stage when I run nvt.mpd it will break it initial stage. And
all 36 chain aligned like output structure.

*gmx_mpi pdb2gmx -f (filename).pdb -o (filename).gro -water spce -missing*

*gmx_mpi editconf -f test_fibril_processed.gro -o
test_fibril_newbox.gro -c -d 1.0 -bt cubic *(This box set-up command)

I also attached nvt.mdp, npt.mdp and md.mdp file. This simulation is
trial run for long time simulation. How should i restrain the position
of my structure.


In the dropbox link i attached nvt.mdp, npt.mdp, md.mdp and also Input
and output structure image in vmd.

https://www.dropbox.com/sh/skkskzp1pruf227/AADI2a7TG6pzadFzIEE8094na?dl=0

Thank you very much.



Please upload the actual coordinate files and any relevant topologies.  I don't 
see how setting up that structure in a cubic box would lead to such a structure.


-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

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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[gmx-users] Position restrain of of different chain in fibril structure

[Md. Imrul Reza Shishir]

Dear all
I have a structure file of cellulose nano fibril of 36 chain (each have 40
residue). I want to simulate it as a single compound. I try to run the
simulation with OPLS-AA force field. After energy minimization when i run
the equilibrium step then the fibril structure broken and all the chain
aligned in a single chain like structure. I want to restrain the position
of chain in there original sheet like structure. But I am  not able to
define.

In the dropbox i attached my simulation structure image file. Initially, it
was 7 sheet of 36 cellulose chain (each chain 40 residues). I check the
structure (gro file) every stage in VMD after new box creation, solvating,
energy minimization. The initial structure is not broken. But after
equilibrium stage when I run nvt.mpd it will break it initial stage. And
all 36 chain aligned like output structure.

*gmx_mpi pdb2gmx -f (filename).pdb -o (filename).gro -water spce -missing*

*gmx_mpi editconf -f test_fibril_processed.gro -o
test_fibril_newbox.gro -c -d 1.0 -bt cubic *(This box set-up command)

I also attached nvt.mdp, npt.mdp and md.mdp file. This simulation is
trial run for long time simulation. How should i restrain the position
of my structure.


In the dropbox link i attached nvt.mdp, npt.mdp, md.mdp and also Input
and output structure image in vmd.

https://www.dropbox.com/sh/skkskzp1pruf227/AADI2a7TG6pzadFzIEE8094na?dl=0

Thank you very much.

-- 
*Md Imrul Reza Shishir*
Master Student
*Inha University*
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[gmx-users] DPPC-DOTAP Mixed Lipid Bilayer

[Nidhin Thomas]

Hi GROMACS Users,

I would like to create a mixed bilayer of DPPC and DOTAP lipids for
research. I usually use charm-gui or insane.py to create a mixed bilayer.
But I could not find DOTAP listed in either of these lists. When I searched
online, I got a mixed bilayer system for DMPC & DPPC lipids and the
parameter file for DOTAP lipid from http://www.softsimu.net/downloads.shtml.

My objective is to create mixed lipid bilayer system with various
percentage of DOTAP lipids. In addition, I have to create a bilayer with
one DOTAP in each layer and remaining DPPC lipids. Can anyone please guide
me to create these lipid bilayers? It would be great if someone could
explain, how to create these mixed bilayers from scratch.

Thanks a lot everyone!,

Nidhin Thomas
University of Houston
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[gmx-users] gmx gangle selections help

[Eric Smoll]

Hello gromacs users,

I want to map the angle between a specific bond vector (defined by the
atoms A and B) and the z axis using gmx gangle. I am only interested in
bond vectors that have a center-of-mass z-coordinate greater than C. Is
there a way to make this selection using the 'gmx select'-type statements?
I suspect that the selection below will not produce an appropriately paired
set of bond atoms. Am I correct?

-g1 vector
-g2  z
-group1 ''resname LIG and name A B and part_res_com z > C"

Best,
Eric
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[gmx-users] Non-bonded energy

[ABANTIKA PAL]

Hi,

I want to know which atoms are to be considered while calculating non-bonded 
energy of a protein. Whether it is all pair atom or there is a particular 
criteria while selecting the atoms.

Thanks.

Abantika
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