Re: [gmx-users] Regarding wired RDF of TMAO and Aminoacid

2017-10-07 Thread Dilip H N 
1*]Regarding the shrinking of the box length:-*

(a)In the npt.mdp file, i am keeping the line [define = -DPOSRES; position
restrain the protein], and running the simulation and after this for npt
production md run (nptmd.mdp, where there is no position restrain). And
after this, if i compare the two files (npt.gro and nptmd.gro), the box
length is further decreased in the nptmd.gro file.
(b) But, if in the npt.mdp file if i remove the position restrain
(-DPOSRES), and then run the simulation, followed by npt proproduction md
run, and then compare the two files (npt.gro and nptmd.gro), the box length
is decreased very slightly (ie., the values are changed in the second/third
decimal point, which is i hope acceptable.)


2]*Regarding the commands:-*

(a)  creating/generating the box with aminoacid:- gmx editconf -f
aminoacid.gro -o aminoacidbox.gro -c -b 2 2 2 (where 2 is the box length)
(b)  inserting the TMAO molecules to the box:- gmx insert-molecules -f
aminoacidbox.gro -ci tmao.gro -nmol 26 -o aminoacidtmao.gro
(c) Solvating the mixture with water :- gmx solvate -cp aminoacidtmao.gro
-cs spc216.gro -o aminoacidtmaowater.gro -maxsol 229
Here I am adding water molecules to the previously added aminoacidtmao
mixture.
I am keeping the number of aminoacid constant, and varying the numbers
of tmao and water molecules to get different concentrations [in this case,
26 molecules of tmao (-nmol 26) and 229 molecules of water (-maxsol 229),
and in other mixtures the tmao and water molecules are changed ].
So, Ideally, in the RDF's, the peak positions must be same but only change
in the heights of the solvation shells, since due to the varying
concentrations. But in my case, i am getting different peaks, for varying
the concentrations, hence i am not getting the analogy...

3] I am running the simulations again and after plotting the RDF's and
i will post the RDF's in the link mentioned...

Thank you...


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On Sat, Oct 7, 2017 at 2:54 AM, Christopher Neale <
chris.ne...@alum.utoronto.ca> wrote:

> 1) take one of your systems, repeat the setup with different random seeds,
> run another 20 ns and make the RDF
>
>
> 2) post the two RDFs of different runs with the same concentrations here:
> http://photobucket.com/
>
> 3) reply to this list with a link to your image and explain what it is
> about your results that don't make sense to you.
>
> Beyond that, the only thing that I can suggest is that it looks bizarre
> that you use the -maxsol option when you add water. You mention that your
> box "keeps shrinking" so perhaps you do have an issue. Normally one would
> add water at full density after adding a variable number of TMAO to get
> different TMAO concentrations (i.e., vary the initial concentration of TMAO
> not the initial concentration of water).
>
> And if you want to send commands, then the XX placeholders are really
> making it hard to know what you are doing. Actual commands are better.
>
> I'm going to leave this thread at this point. Feel free to PM me to let me
> know that you have posted your images to photobucked and put a link on the
> gmx list and I will take a look and reply on list.
> 
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Dilip H N
> <cy16f01.di...@nitk.edu.in>
> Sent: 06 October 2017 02:39:49
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Regarding wired RDF of TMAO and Aminoacid
>
> 1] My simulations in the production MD are for 10 ns. I am first doing
> energy minimization, followed by NPT run of 2ns (100; 0.002 * 100 =
> 2000 ps[2ns]), and then followed by NPT Production MD run for 10 ns
> (1000; 0.001 * 1000 = 1 ps [10 ns]). During the npt simulation,
> the box length is reducing, and further during the nptmd ie., production
> md too the box length is getting reduced still further. I am not getting
> any idea over this... Is the time duration enough or still i need to do it
> for more timestep..??
>
> 2] Regarding the commands i use to get the mixtures into the simulation box
> are:-
> (a)  creating the box:- gmx editconf -f abc.gro -o abcbox.gro -c -b X X X
> (b)  inserting the molecules:- gmx insert-molecules -f abcbox.gro -ci
> def.gro -nmol X -o ghi.gro
> (c) Solvating the mixture with water :- gmx solvate -cp ghi.gro -cs
> spc216.gro -o jkl.gro -maxsol XXX
> So these are the commands which i give in order to generate my Simulation
> box containing Amino acid, TMAO and Water mixture.
> Hope these are the right set of commands... and then i start
> simulation...EM followed by NPT followed by NPTMD...
>
> Th

Re: [gmx-users] Regarding wired RDF of TMAO and Aminoacid

2017-10-06 Thread Christopher Neale 
1) take one of your systems, repeat the setup with different random seeds, run 
another 20 ns and make the RDF


2) post the two RDFs of different runs with the same concentrations here: 
http://photobucket.com/

3) reply to this list with a link to your image and explain what it is about 
your results that don't make sense to you.

Beyond that, the only thing that I can suggest is that it looks bizarre that 
you use the -maxsol option when you add water. You mention that your box "keeps 
shrinking" so perhaps you do have an issue. Normally one would add water at 
full density after adding a variable number of TMAO to get different TMAO 
concentrations (i.e., vary the initial concentration of TMAO not the initial 
concentration of water).

And if you want to send commands, then the XX placeholders are really making it 
hard to know what you are doing. Actual commands are better.

I'm going to leave this thread at this point. Feel free to PM me to let me know 
that you have posted your images to photobucked and put a link on the gmx list 
and I will take a look and reply on list.

From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
<gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Dilip H N 
<cy16f01.di...@nitk.edu.in>
Sent: 06 October 2017 02:39:49
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Regarding wired RDF of TMAO and Aminoacid

1] My simulations in the production MD are for 10 ns. I am first doing
energy minimization, followed by NPT run of 2ns (100; 0.002 * 100 =
2000 ps[2ns]), and then followed by NPT Production MD run for 10 ns
(1000; 0.001 * 1000 = 1 ps [10 ns]). During the npt simulation,
the box length is reducing, and further during the nptmd ie., production
md too the box length is getting reduced still further. I am not getting
any idea over this... Is the time duration enough or still i need to do it
for more timestep..??

2] Regarding the commands i use to get the mixtures into the simulation box
are:-
(a)  creating the box:- gmx editconf -f abc.gro -o abcbox.gro -c -b X X X
(b)  inserting the molecules:- gmx insert-molecules -f abcbox.gro -ci
def.gro -nmol X -o ghi.gro
(c) Solvating the mixture with water :- gmx solvate -cp ghi.gro -cs
spc216.gro -o jkl.gro -maxsol XXX
So these are the commands which i give in order to generate my Simulation
box containing Amino acid, TMAO and Water mixture.
Hope these are the right set of commands... and then i start
simulation...EM followed by NPT followed by NPTMD...

Thank you...

With Best Regards,

DILIP.H.N
Ph.D Student


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With Best Regards,

DILIP.H.N
Ph.D Student
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Re: [gmx-users] Regarding wired RDF of TMAO and Aminoacid

2017-10-06 Thread Dilip H N 
1] My simulations in the production MD are for 10 ns. I am first doing
energy minimization, followed by NPT run of 2ns (100; 0.002 * 100 =
2000 ps[2ns]), and then followed by NPT Production MD run for 10 ns
(1000; 0.001 * 1000 = 1 ps [10 ns]). During the npt simulation,
the box length is reducing, and further during the nptmd ie., production
md too the box length is getting reduced still further. I am not getting
any idea over this... Is the time duration enough or still i need to do it
for more timestep..??

2] Regarding the commands i use to get the mixtures into the simulation box
are:-
(a)  creating the box:- gmx editconf -f abc.gro -o abcbox.gro -c -b X X X
(b)  inserting the molecules:- gmx insert-molecules -f abcbox.gro -ci
def.gro -nmol X -o ghi.gro
(c) Solvating the mixture with water :- gmx solvate -cp ghi.gro -cs
spc216.gro -o jkl.gro -maxsol XXX
So these are the commands which i give in order to generate my Simulation
box containing Amino acid, TMAO and Water mixture.
Hope these are the right set of commands... and then i start
simulation...EM followed by NPT followed by NPTMD...

Thank you...

With Best Regards,

DILIP.H.N
Ph.D Student


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With Best Regards,

DILIP.H.N
Ph.D Student
-- 
Gromacs Users mailing list

* Please search the archive at 
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Re: [gmx-users] Regarding wired RDF of TMAO and Aminoacid

2017-10-04 Thread Christopher Neale 
Please show us the plots (upload to a file hosting site and paste the link in 
your post) or precisely define your results; also explain precisely why the 
results are unexpected. Also show us your exact commands. Without this we can 
not help.


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
<gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Dilip H N 
<cy16f01.di...@nitk.edu.in>
Sent: 04 October 2017 23:48:08
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] Regarding wired RDF of TMAO and Aminoacid

Hello,
I have run an NPT MD simulation of an amino acid with TMAO (as a cosolvent)
and water for different concentration (by varying composition of cosolvent:
water). I have used Charmm36 FF for TMAO.
Now if i am plotting the RDF for Amino acid v/s Water in the presence of
different concentrations TMAO, I am getting wired RDF's for each
composition of TMAO present, the peaks are absurd.
Why is this happening..?? i have looked into the final structure of my
simulation in VMD which is correct
I am confused...
Any Suggestions are appreciated...


--
With Best Regards,

DILIP.H.N
Ph.D Student



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[gmx-users] Regarding wired RDF of TMAO and Aminoacid

2017-10-04 Thread Dilip H N 
Hello,
I have run an NPT MD simulation of an amino acid with TMAO (as a cosolvent)
and water for different concentration (by varying composition of cosolvent:
water). I have used Charmm36 FF for TMAO.
Now if i am plotting the RDF for Amino acid v/s Water in the presence of
different concentrations TMAO, I am getting wired RDF's for each
composition of TMAO present, the peaks are absurd.
Why is this happening..?? i have looked into the final structure of my
simulation in VMD which is correct
I am confused...
Any Suggestions are appreciated...


-- 
With Best Regards,

DILIP.H.N
Ph.D Student



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