Re: [gmx-users] (no subject)

[Rakesh Mishra]

Hi Mark

Did you get the point or  not .
Hoping your  response

On Fri, Aug 31, 2018 at 6:17 PM, Rakesh Mishra  wrote:

>
> *Please remember (its your  query to me )*
> Hi,
>
> Can you please share a link to something that indicates why this would be a
> good tool for modeling such experimental pulling scenarios? Making the case
> for implementing such a feature would benefit from that.
>
> Mark
> >  dt)+-+t2,+e=gmail=g
> 
> >
>
>
>
> *This is our response *
>
>
> Dear Mark,
>
> There are several experiments have been done for protein and DNA
> unfolding.
> Thy  became pioneer in this field.  That is why force should apply and
> corresponding reaction
> coordinates are measured . Here Gromacs login do not allow to upload
> larger data.
> But I can mention some paper address . If get time Please go through these
> papers .
>
> 1- NATURE | VOL 421 | 23 JANUARY 2003 | www.nature.com/nature (Carlos
> Bustamante*†, Zev Bryant* & Steven B. Smith†)
>
> 2-  SCIENCE 1⁄7 VOL. 275 1⁄7 28 FEBRUARY 1997 (Matthias Rief, Filipp
> Oesterhelt, Berthold Heymann,Hermann E. Gaub )
>
> That is  why I  asked about force-extension protocol.  In Umbrella
> sampling distance is increases linearly with the time and corresponding
> force experienced by the system writes .
>
> We still don't no that force/time which writes in .xvg file corresponds
> which formula like f= k(vt-x) or something else.
> There are other lot experiments regarding measurement of stability of the
> DNA and protein under f/x curve.
> One can see some theory paper also to see f/x like.
>
> 1- THE JOURNAL OF CHEMICAL PHYSICS 148, 215105 (2018)
>
>
>
>
> Note- According to Justin one  can write that protocol. If suppose we
> write that protocol, then how  to apply in gromacs.
>
> There are only input .mdp files. We didn't know  where to built the force
> subroutine in .ff (force field ) directory. or somewhere else.
>
>
> Hoping for  response.
>
>
>
>
>
>
> On Fri, Aug 31, 2018 at 6:08 PM, Rakesh Mishra 
> wrote:
>
>> Dear  mark
>> I had already discussed regarding force/extension protocol.
>> But I didn't get any response from your side. I dont have
>> idea to upload some pictures.
>>
>> On Fri, Aug 31, 2018 at 4:05 PM, Mark Abraham 
>> wrote:
>>
>>> Hi,
>>>
>>> The list cannot accept attachments. Upload to a file sharing service and
>>> share a link. We will likely need more background information also.
>>>
>>> Mark
>>>
>>> On Fri, Aug 31, 2018, 12:22 Rakesh Mishra  wrote:
>>>
>>> > Hi every body
>>> > can any one  explain what is the mean of this graph
>>> > obtained from gromacs  constant velocity pulling of dsDNA
>>> > along the helical direction. (force.xvg). Basically sudden drop of
>>> force
>>> > represents what ?
>>> > --
>>> > Gromacs Users mailing list
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>>
>>
>>
>> --
>>
>> *With Best-Rakesh Kumar Mishra*
>> *  (RA)CSD  SINP Kolkata, India*
>>
>> *E-mail - rakesh.mis...@saha.ac.in  *
>>
>> *Phone n. +91 9473662491, +918777496532*
>>
>
>
>
> --
>
> *With Best-Rakesh Kumar Mishra*
> *  (RA)CSD  SINP Kolkata, India*
>
> *E-mail - rakesh.mis...@saha.ac.in  *
>
> *Phone n. +91 9473662491, +918777496532*
>



-- 

*With Best-Rakesh Kumar Mishra*
*  (RA)CSD  SINP Kolkata, India*

*E-mail - rakesh.mis...@saha.ac.in  *

*Phone n. +91 9473662491, +918777496532*
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Re: [gmx-users] Combining edr files for NPT with different dt values

[Stephani Macalino]

Hello,
Thanks for your prompt response!
I am doing this since I am following the gromacs tutorial of checking the
pressure and density stabilization of my system (I'm a newbie).
I just found one instruction where it mentioned about doing interactive
commands (
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2011-April/060733.html
),
i.e. using a .txt file with 'c' for each line (depending on the number of
edr files) and -settime as you have mentioned.
This solution has worked for me.
Thanks again!
Regards,
Stephani

On Mon, 3 Sep 2018 at 12:08, Mark Abraham  wrote:

> Hi,
>
> You'll have to look more closely at the way you tried to concatenate them
> and see why the file you eventually gave to gmx energy had only 2ns. For
> example, if each check treated its first step as time zero, then you need
> to consider gmx eneconv -settime, etc. But I wouldn't bother with any of
> this for equilibration. If the last segment is consistent with the ensemble
> you seek, then that is the job done.
>
> Mark
>
> On Mon, Sep 3, 2018 at 2:11 AM Stephani Macalino <
> stephanimacal...@gmail.com>
> wrote:
>
> > Hello,
> > I am trying to combine edr files using the gmx eneconv command.
> > I did 6 cycles of equilibration (1 NVT and 5 NPT). The NPT cycles are 2ns
> > each but the first 2 have a dt of 0.001 while the last 4 have dt of
> 0.002.
> > I tried to combine them and check the density using gmx energy command
> but
> > I keep getting a file with only 2ns of time included, when it should be
> > 10ns.
> > I thought maybe because the dt is different, but when I only combined the
> > first 2, I still only got 2ns instead of 4ns.
> > All other parameters are the same for the mdp files of each equilibration
> > cycle. The only difference are the dt and force constants used.
> > How can I combine these files so I can analyze my pressure and density
> > graphs?
> > Hope you can help.
> > Thank you!
> > Regards,
> > Stephani
> > --
> > 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] Combining edr files for NPT with different dt values

[Mark Abraham]

Hi,

You'll have to look more closely at the way you tried to concatenate them
and see why the file you eventually gave to gmx energy had only 2ns. For
example, if each check treated its first step as time zero, then you need
to consider gmx eneconv -settime, etc. But I wouldn't bother with any of
this for equilibration. If the last segment is consistent with the ensemble
you seek, then that is the job done.

Mark

On Mon, Sep 3, 2018 at 2:11 AM Stephani Macalino 
wrote:

> Hello,
> I am trying to combine edr files using the gmx eneconv command.
> I did 6 cycles of equilibration (1 NVT and 5 NPT). The NPT cycles are 2ns
> each but the first 2 have a dt of 0.001 while the last 4 have dt of 0.002.
> I tried to combine them and check the density using gmx energy command but
> I keep getting a file with only 2ns of time included, when it should be
> 10ns.
> I thought maybe because the dt is different, but when I only combined the
> first 2, I still only got 2ns instead of 4ns.
> All other parameters are the same for the mdp files of each equilibration
> cycle. The only difference are the dt and force constants used.
> How can I combine these files so I can analyze my pressure and density
> graphs?
> Hope you can help.
> Thank you!
> Regards,
> Stephani
> --
> 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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[gmx-users] Combining edr files for NPT with different dt values

[Stephani Macalino]

Hello,
I am trying to combine edr files using the gmx eneconv command.
I did 6 cycles of equilibration (1 NVT and 5 NPT). The NPT cycles are 2ns
each but the first 2 have a dt of 0.001 while the last 4 have dt of 0.002.
I tried to combine them and check the density using gmx energy command but
I keep getting a file with only 2ns of time included, when it should be
10ns.
I thought maybe because the dt is different, but when I only combined the
first 2, I still only got 2ns instead of 4ns.
All other parameters are the same for the mdp files of each equilibration
cycle. The only difference are the dt and force constants used.
How can I combine these files so I can analyze my pressure and density
graphs?
Hope you can help.
Thank you!
Regards,
Stephani
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[gmx-users] Water properties above surface

[rose rahmani]

Hi,

I study the interaction of different amino acid above surface in presence
of (TIP3P)water in physiological ion concentration(150mM) and i calculated
PMF for different distances of AA above surface.
Now, i want to find different proofs which prove the importance of water
molecules, amino acids different polarities and hydrophobicities and water
layer formed above surface in the quality of AA interaction with surface.
I searched about every tools in lovely GROMACS to calculate these
properties; So,

1- We all know about different amino acids properties(polarity,
hydrophobicity, ...) generally, but i could not find any tool in GROMACS to
quantitively prove these properties (amino acids) in different systems.
However i think it is not possible at all;) , we should search about
different clues,... . for example i want to show the distribution of water
in RADIAL distances around AA  to show the hydrophobicity/phility but i
don't know which tool can do it? is gmx spol appropeiate for these goals?
( I will refer you to these question's attached filehttps://
www.researchgate.net/post/How_can_i_calculate_the_distribution_of_water_polarization_above_surface
)

2- number density profile of water above surface which causes forming
solvent layers... fortunately i could do it by gmx density. but how about
the orientation of water molecules near the surface? how can i show that?
can gmx hydorder or gmx sorient does?
3- and what i have never understand about gmx SASA is that; for example
when i choose protein and SOL group, what does it exactly calculate? does
it will calculate the solvent area around AA??

sorry for multiple question
I would be grateful if you answer to them.

Best regards

Rose
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[gmx-users] Per species g_energy value

[Apramita Chand]

Dear All,
In my simulation system, I have one peptide with 10 cosolvent molecules and
989 water molecules. I want to have an idea of the interactions energies
between peptide-water, peptide-cosolvent etc. Using g_energy , if I obtain
a total of -687kJ interaction energy between peptide-water, should I divide
the value by no. of water molecules to get the value per water molecule? Or
is it a 'per peptide' value and cannot be divided by no.of water molecules?
Please help.
Yours sincerely
Apramita Chand
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