[gmx-users] Mycobacterium cell wall protein

[Shanmuga Priya V.G]

Dear Gromacs Users,
I have a insilico model of Mycobacterium tuberculosis cell wall  (surface)
protein
which has no transmembrane helices. Which Gromacs tutorials should I
follow for MD studies to know about its conformational stability and
latter for protein - ligand studies. Kindly guide me

Thanking you

with regards
V.G.Spriya

KLE Dr.MSSCET,Belgaum
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Re: [gmx-users] CG-MD to study the conformational changes of proteins...

[Shanmuga Priya V.G]

Dear Gromacs Users,
I have a insilico model of Mycobacterium cell wall  (surface) protein
which has no transmembrane helices.Which Gromacs tutorials should I
follow for MD studies to know about its conformational stability and
latter for protein - ligand studies. Kindly guide me

Thanking you

with regards
V.G.Shanmuga Priya

On Mon, Dec 26, 2016 at 11:06 PM, Dariush Mohammadyani <
d.mohammady...@gmail.com> wrote:

> Hi Quyen,
>
> Although Martini is a good CG force field for a system contains lipids and
> proteins, it still needs some improvements to capture conformational
> changes (especially large changes).
> Is there any hybrid model available (and ready to use) for such a system?
>
>
> Regards,
> Dariush
>
> On Mon, Dec 26, 2016 at 11:23 AM, Quyen V. Vu  wrote:
>
> > Nikhil say:
> >
> > I would like to study the conformational study of proteins (Amyloid beta)
> > in presence of lipid bilayers and other molecules. Can anyone tell me the
> > possibility of Coarse-grained molecular dynamics for this study, since
> > all-atom MD need more time and my system contains more atoms, so I'm
> > thinking to go for CGMD.  in CG-MD can we do the same analysis as in
> > All-atom MD.?
> >
> >
> > You need to find a force field that support for protein coarse-grain
> model
> >
> > such as Martini: http://cgmartini.nl/
> >
> > to save simulation time you can you CG model or hybrid model( result
> > better than CG model because a important region
> >
> > is treated as standard MD, less important region is use CG model
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Re: [gmx-users] viscosity using green kubo relation for ionic liquids

[Shanmuga]

But in energy file we don't have stress tensor and some how we have to 
calculate stress tensor from pressure tensor. I am wondering how to get stress 
tensor from pressure tensor, in liquid md simulations. 

Regards, 
Shanu 

Sent from my iPhone

> On Jan 13, 2016, at 3:41 PM, David van der Spoel <sp...@xray.bmc.uu.se> wrote:
> 
>> On 13/01/16 18:11, Shanmuga wrote:
>> Hi all,
>> 
>> I am comparing viscosity calculation with eq md and non eq md. I want to 
>> calculate viscosity in eq md with green kubo equation. Can anyone suggest me 
>> how to get stress tensor from pressure tensor and its auto correction plot.
>> 
> Still gmx energy. Check all the options.
>> Thanks in advance.
>> 
>> Regards,
>> Shanu
>> 
>>> On Jan 12, 2016, at 3:35 PM, VITALY V. CHABAN <vvcha...@gmail.com> wrote:
>>> 
>>> EqMD methods work poorly for highly and moderate viscous liquids.
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> On Tue, Jan 12, 2016 at 5:19 PM, shanmuga sundaram <shanmugam...@gmail.com>
>>> wrote:
>>> 
>>>> I tried with g_energy -vis , but it calculates using einstein relation. I
>>>> want to calculate using green kubo equation.
>>>> 
>>>> 
>>>> regards,
>>>> 
>>>> shanu
>>>> 
>>>> On Tue, Jan 12, 2016 at 12:42 AM, David van der Spoel <
>>>> sp...@xray.bmc.uu.se>
>>>> wrote:
>>>> 
>>>>>> On 11/01/16 22:54, shanmuga sundaram wrote:
>>>>>> 
>>>>>> Hello all,
>>>>>> 
>>>>>> 
>>>>>> I am trying to find viscosity using green kubo relation for Ionic
>>>> Liquids.
>>>>>> I got pressure tensor values (pxx, pyy, pzz, ….) from energy file .edr.
>>>>>> How
>>>>>> to get stress autocorrelation function (SACF) from pressure
>>>>>> autocorrelation
>>>>>> function in MD simulations? Also how to change ACF windows (10, 50,
>>>> 200ps)
>>>>>> in getting autocorrelation function from gromacs (usually from g_analyze
>>>>>> tool)?
>>>>>> 
>>>>>> try
>>>>> g_energy -vis
>>>>> 
>>>>> 
>>>>>> regards,
>>>>>> 
>>>>>> shanu
>>>>> 
>>>>> --
>>>>> David van der Spoel, Ph.D., Professor of Biology
>>>>> Dept. of Cell & Molec. Biol., Uppsala University.
>>>>> Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
>>>>> sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
>>>>> --
>>>>> 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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>>>>> 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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>>>> posting!
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>>> --
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> 
> 
> -- 
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:+46184714205.
> sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
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Re: [gmx-users] viscosity using green kubo relation for ionic liquids

[Shanmuga]

Hi all, 

I am comparing viscosity calculation with eq md and non eq md. I want to 
calculate viscosity in eq md with green kubo equation. Can anyone suggest me 
how to get stress tensor from pressure tensor and its auto correction plot. 

Thanks in advance. 

Regards, 
Shanu

> On Jan 12, 2016, at 3:35 PM, VITALY V. CHABAN <vvcha...@gmail.com> wrote:
> 
> EqMD methods work poorly for highly and moderate viscous liquids.
> 
> 
> 
> 
> 
> 
> On Tue, Jan 12, 2016 at 5:19 PM, shanmuga sundaram <shanmugam...@gmail.com>
> wrote:
> 
>> I tried with g_energy -vis , but it calculates using einstein relation. I
>> want to calculate using green kubo equation.
>> 
>> 
>> regards,
>> 
>> shanu
>> 
>> On Tue, Jan 12, 2016 at 12:42 AM, David van der Spoel <
>> sp...@xray.bmc.uu.se>
>> wrote:
>> 
>>>> On 11/01/16 22:54, shanmuga sundaram wrote:
>>>> 
>>>> Hello all,
>>>> 
>>>> 
>>>> I am trying to find viscosity using green kubo relation for Ionic
>> Liquids.
>>>> I got pressure tensor values (pxx, pyy, pzz, ….) from energy file .edr.
>>>> How
>>>> to get stress autocorrelation function (SACF) from pressure
>>>> autocorrelation
>>>> function in MD simulations? Also how to change ACF windows (10, 50,
>> 200ps)
>>>> in getting autocorrelation function from gromacs (usually from g_analyze
>>>> tool)?
>>>> 
>>>> try
>>> g_energy -vis
>>> 
>>> 
>>>> regards,
>>>> 
>>>> shanu
>>> 
>>> --
>>> David van der Spoel, Ph.D., Professor of Biology
>>> Dept. of Cell & Molec. Biol., Uppsala University.
>>> Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
>>> sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
>>> --
>>> 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] viscosity using green kubo relation for ionic liquids

[shanmuga sundaram]

I tried with g_energy -vis , but it calculates using einstein relation. I
want to calculate using green kubo equation.


regards,

shanu

On Tue, Jan 12, 2016 at 12:42 AM, David van der Spoel <sp...@xray.bmc.uu.se>
wrote:

> On 11/01/16 22:54, shanmuga sundaram wrote:
>
>> Hello all,
>>
>>
>> I am trying to find viscosity using green kubo relation for Ionic Liquids.
>> I got pressure tensor values (pxx, pyy, pzz, ….) from energy file .edr.
>> How
>> to get stress autocorrelation function (SACF) from pressure
>> autocorrelation
>> function in MD simulations? Also how to change ACF windows (10, 50, 200ps)
>> in getting autocorrelation function from gromacs (usually from g_analyze
>> tool)?
>>
>> try
> g_energy -vis
>
>
>> regards,
>>
>> shanu
>>
>>
>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
> sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
> --
> Gromacs Users mailing list
>
> * Please search the archive at
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[gmx-users] viscosity using green kubo relation for ionic liquids

[shanmuga sundaram]

Hello all,


I am trying to find viscosity using green kubo relation for Ionic Liquids.
I got pressure tensor values (pxx, pyy, pzz, ….) from energy file .edr. How
to get stress autocorrelation function (SACF) from pressure autocorrelation
function in MD simulations? Also how to change ACF windows (10, 50, 200ps)
in getting autocorrelation function from gromacs (usually from g_analyze
tool)?


regards,

shanu
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[gmx-users] ionic liquids - viscosity using green kubo relation

[shanmuga sundaram]

Hello all,


I am trying to find viscosity using green kubo relation for Ionic Liquids.
I got pressure tensor values (pxx, pyy, pzz, ….) from energy file .edr. How
to get stress autocorrelation function (SACF) from pressure autocorrelation
function in MD simulations? Also how to change ACF windows (10, 50, 200ps)
in getting autocorrelation function from gromacs (usually from g_analyze
tool)?


regards,

shanu
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