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

[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.neale at 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-bounces at maillist.sys.kth.se <
> gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Dilip H N
> <cy16f01.dilip at nitk.edu.in>
> Sent: 06 October 2017 02:39:49
> To: gmx-users at 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 (1000000; 0.002 * 1000000 =
> 2000 ps[2ns]), and then followed by NPT Production MD run for 10 ns
> (10000000; 0.001 * 10000000 = 10000 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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-- 
With Best Regards,

DILIP.H.N
Ph.D Student