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

Christopher Neale chris.neale at alum.utoronto.ca
Fri Oct 6 23:24:38 CEST 2017

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
(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,

Ph.D Student

<https://mailtrack.io/> Sent with Mailtrack

With Best Regards,

Ph.D Student
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