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

[Christopher Neale]

Personally, I would still have to see the RDFs to have any idea of how to help. If you don't want to or can not share them, then I suggest running a few repeat simulations (different starting conditions, with different initial placement of TMAO) at the low TMAO concentration and seeing if you get similar results in the repeats. In the absence of evidence that there is something truly bizarre going on, my guess is that you may just be seeing convergence issues at low TMAO concentrations with short simulations (how long are they?)

________________________________
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: 05 October 2017 23:53:03
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Regarding wired RDF of TMAO and Aminoacid

Sir,
1] Regarding the unexpected results, i meant that for different
concentrations, the peaks should be same, but only its height/well  of the
solvation shells differs (since there will be only variation  in
concentration), but in my case, there are different solvation shells,
except the first solvation shell, other solvations shells that i see are
wired...hence i am not getting the analogy...

2] Regarding the commands:-
(a) making indexes:- gmx make_ndx -f nptmd.gro -o abc.ndx
     and after this i delete all the groups, and manually add the atoms
that i need (since i can avoid other atoms in the index file i am
creating)by using commands as:- a N (or) ri 1 & a N enter a OW (or) HW1 HW2
enter q
(b) calculating RDF and CN:- gmx rdf -f nptmd.trr -s nptmd.tpr -n abc.ndx
-o rdf_abc.xvg -cn cn_abc.xvg -ref 0 -sel 1
which calculates the RDF and CN...
These are the commands that i am following...

Thank you...




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<#>

On Thu, Oct 5, 2017 at 11:16 AM, Christopher Neale <
chris.neale at alum.utoronto.ca> wrote:

> 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-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: 04 October 2017 23:48:08
> To: gromacs.org_gmx-users at 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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--
With Best Regards,

DILIP.H.N
Ph.D Student
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