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 <jalem...@vt.edu>
*받는사람(To) :* gmx-us...@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
jalem...@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
jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com
==================================================
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