[gmx-users] Heavy water H-H radial distribution function

Thu Jun 21 01:10:43 CEST 2018

Please keep the discussion on the gmx-users mailing list. I don't have 
time to offer personal GROMACS help.

On 6/18/18 9:42 PM, Haelee Hyun wrote:
>
> Dear Justin,
>
> Thank you for your response about my question.
>
> I'm writing this email to ask something more.
> The image file of the H-H rdf wasn't atteched in last email.
>
> So I hope you would check this files....
>
> HH_rdf.PNG file is calculated result from my GROMACS simulation And 
> Soper_HH_rdf.PNG file is the experimental data.
>

Separate plots on different scales are very difficult to interpret. I 
don't really have any insight into what is going on.

If you wish to share images and/or files with the list, upload them to a 
file-sharing service and provide the URL.

> As i said last email, the first peak from the intramolecular 
> interaction shows big difference.
>
> I need to correctly describe this first peak...i've used -excl flag 
> after reading your advice but my problem was to solve this big 
> peak that shows much bigger than the experimental data.
>

The -excl flag should have taken care of this, so I don't know why 
you're still getting what appears to be a very clear intramolecular 
peak. But then, too, the experimental data seem to include this peak as 
well, but again what you provided was hard to interpret.

> I guess this problem is caused by wrong parameters describing 
> intramolecular interaction.
>

Possible, but you should start with reproducing a known outcome before 
moving into weird things like flexible water with heavy H atoms. I don't 
see anything actually suspect with what you've plotted.

-Justin

> So i've tried to run GROMACS simulation with various .mdp options.
>
> But I couldn't find the problem.
>
> If you have some idea about the intramolecular interaction or anything 
> else, please let me know.
>
> I hope I'm not trespassing on your time.
>
> Thank you for reading my email.
>
>
> Best regards,
>
> Haelee Hyun
>
>
>
>
>
> -----Original Message-----
>
>     *보낸사람(From) :* Justin Lemkul <jalemkul at vt.edu>
>     *받는사람(To) :* gmx-users at gromacs.org,
>     *보낸일자(Sent) :* 2018-06-19 03:59:18
>     *메일제목(Subject) :* Re: [gmx-users] Heavy water H-H radial
>     distribution function
>
>
>
>
>     On 6/18/18 3:47 AM, Haelee Hyun wrote:
>     >
>     > Dear GROMACS users,
>     >
>     > I'm wondering how?can I correctly?describe H-H radial distribution
>     > function of heavy water.
>     >
>     > Please check atteched file HH_rdf.PNG which is?a
>     calculated?result of
>     > H-H radial distribution?from my simulation.
>     >
>
>     The list does not accept attachments.
>
>     > The first?peak is due to the intramolecular interaction of water
>     > molecules.
>     >
>     > It shows?almolst 7?at 0.13 nm but when?comparing this result
>     with an
>     > experimental data, the experimental data shows just almost 2 at the
>     > first peak.
>     >
>     > I have tried?many times of simulations but i couldn't find why this
>     > huge?difference is caused.
>     >
>     > I used tip4p/2005f water model and used potential is atteched
>     below.
>     >
>
>     You need to use the -excl flag to read topology exclusions. Doing so
>     will get rid of this intramolecular peak.
>
>     -Justin
>
>     > [ defaults ]
>     > ; nbfunc?comb-rule?gen-pairs?fudgeLJ?fudgeQQ
>     > 1??3??yes??0.5?0.5
>     >
>     > [ moleculetype ]
>     > ; molname?nrexcl
>     > SOL??2
>     >
>     > [ atoms ]
>     > ; id?at type?res nr ?residu name?at name?cg nr?charge
>     > 1?????? opls_113??????? 1?????? SOL????? OW???? 1?????? 0.0
>     > 2?????? opls_114??????? 1?????? SOL???? HW1???? 1?????? 0.5564
>     > 3?????? opls_114??????? 1?????? SOL???? HW2???? 1?????? 0.5564
>     > 4?????? opls_115??????? 1?????? SOL????? MW???? 1????? -1.1128
>     >
>     > ;[nonbond_params]
>     > ; i?j?funct?q?????????? V??????????? W
>     > ;1?2?1?0.5564????? 3.16440e-01? 7.74907e-01
>     > ;1?3?1?????? 0.5564????? 3.16440e-01? 7.74907e-01
>     >
>     >
>     > #ifndef FLEXIBLE
>     > [ settles ]
>     > ; OW??? funct?? doh??????? dhh
>     > 1?????? 1?????? 0.09664??? 0.15555
>     >
>     > #else
>     >
>     > [ bonds ]
>     > ; i?j?funct?length?? D?????? beta
>     > 1?2????? 3??? 0.09419?? 432.581?? 22.87?? ; For TIP4P/2005f
>     Water b0,
>     > D, beta
>     > 1?3????? 3??? 0.09419?? 432.581?? 22.87?? ; For TIP4P/2005f
>     Water b0,
>     > D, beta
>     >
>     > [ angles ]
>     > ; i?j?k?funct?angle?force.c.
>     > 2?1?3?1?107.4?367.81
>     > #endif
>     >
>     > [ exclusions ]
>     > 1?2?3?4
>     > 2?1?3?4
>     > 3?1?2?4
>     > 4?1?2?3
>     >
>     > ; The position of the virtual site is computed as follows:
>     > ;
>     > ; const = distance (OD) / [ cos (angle(DOH)) ?* distance (OH) ]
>     > ;?? 0.015 nm?/ [ cos (52.26 deg)?* 0.09572 nm?]
>     >
>     > ; Vsite pos x4 = x1 + a*(x2-x1) + b*(x3-x1)
>     >
>     > [ virtual_sites3 ]
>     > ; Vsite from???funct?a??b
>     > 4?1?2?3?1?0.13288????? 0.13288
>     >
>     >
>     > I used -DFLEXIBLE option and energy minimization, NVT, NPT
>     > equlibration and NVE production run.
>     >
>     > If someone would?find some wrong things, please let me know.
>     >
>     > Thank you.
>     >
>     > Haelee Hyun
>     >
>     >
>     >
>     >
>     >
>     >
>
>     -- 
>     ==================================================
>
>     Justin A. Lemkul, Ph.D.
>     Assistant Professor
>     Virginia Tech Department of Biochemistry
>
>     303 Engel Hall
>     340 West Campus Dr.
>     Blacksburg, VA 24061
>
>     jalemkul at vt.edu | (540) 231-3129
>     http://www.thelemkullab.com
>
>     ==================================================
>
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-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================