[gmx-users] Re: gmx-users Digest, Vol 22, Issue 91
linfu
linfu3200 at 126.com
Thu Feb 23 01:56:21 CET 2006
gmx-users-request,ÄúºÃ£¡
1. Re: Diffusion Coefficient from VAC (Viswanadham Sridhara)
======= 2006-02-23 04:34:14 ÄúÔÚÀ´ÐÅÖÐдµÀ£º=======
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>Today's Topics:
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> 1. Re: Diffusion Coefficient from VAC (Viswanadham Sridhara)
> 2. Re: Diffusion Coefficient from VAC (Viswanadham Sridhara)
> 3. Re: Re: ewald_rtol and convergence (David van der Spoel)
> 4. Re: Diffusion Coefficient from VAC (Alexandre Suman de Araujo)
>
>
>----------------------------------------------------------------------
>
>Message: 1
>Date: Wed, 22 Feb 2006 14:54:39 -0500
>From: "Viswanadham Sridhara" <muta.mestri at gmail.com>
>Subject: Re: [gmx-users] Diffusion Coefficient from VAC
>To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
>Message-ID:
> <a5e4ea9a0602221154g227d8d0eof036209d23844065 at mail.gmail.com>
>Content-Type: text/plain; charset="iso-8859-1"
>
>Taking the integral of the velocity auto-correlation function multiplied by
>cosine of the angular frequency and scaling it properly should give the
>diffusion coefficient as a function of frequency.
>
>On 2/22/06, Frederic Leroy <frederic.leroy at urv.net> wrote:
>>
>> What do you mean quantatively by "VAC does not agree with one calculated
>> from MSD"?
>>
>>
>>
>> Alexandre Suman de Araujo wrote:
>>
>> > Hi Gmxers.
>> >
>> > I´m trying to calculate coefficient diffusion values for ions in water.
>> >
>> > I made some calculations using MSD and the results were in good
>> > agreement with experimental values.
>> >
>> > The problem is when I try to calculate it from integration of VAC
>> > function for the ions, like in Rasaiah paper (J. Chem Phys. 101(8)
>> 6964).
>> >
>> > I made 40 simulations of 250 ps with 1 fs time step and output of
>> > velocities every 1 fs. From these simulations I calculated the
>> > normalized VAC function from these 40 simulations and calculated the
>> > mean. This methodology is implemented to have a good statistic and a
>> > more smooth VAC function (without fluctuations that could make the
>> > integral diverge). With this VAC function I use this equation to
>> > calculate do diffusion coefficient:
>> >
>> > D = kT/M*Y, where Y is the integral of the VAC function
>> >
>> > The problem is that the value calculated from VAC does not agree with
>> > one calculated from MSD.
>> >
>> > Does anyone knows any trick to perform this kind of calculation? In
>> > the paper cited above these two values are very near and I´m using the
>> > same methodology.
>> >
>> > Thank´s!
>> >
>>
>> _______________________________________________
>> gmx-users mailing list gmx-users at gromacs.org
>> http://www.gromacs.org/mailman/listinfo/gmx-users
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>
>
>
>--
>Viswanadham Sridhara,
>Graduate Research Assistant,
>Old Dominion University, "VIRGINIA".
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>------------------------------
>
>Message: 2
>Date: Wed, 22 Feb 2006 14:57:42 -0500
>From: "Viswanadham Sridhara" <muta.mestri at gmail.com>
>Subject: Re: [gmx-users] Diffusion Coefficient from VAC
>To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
>Message-ID:
> <a5e4ea9a0602221157h7f1005a2ta1ad7979f39b1a59 at mail.gmail.com>
>Content-Type: text/plain; charset="iso-8859-1"
>
>IF it is for pure water (bulk), then mass of the water should be
>m=(18e-3)/Ava, where Ava is the Avogadro number.
>KbT/m works out to be 1.3857e+005;
>
>On 2/22/06, Alexandre Suman de Araujo <asaraujo at if.sc.usp.br> wrote:
>>
>> Yes, I tried and I had bad values too.
>> I think the Kubo equation is to use in the non-normalized VAC, since the
>> D = kT/M*integral is for normalized ones.
>>
>> Alexandre Suman de Araujo
>> asaraujo at if.sc.usp.br
>> UIN: 6194055
>> IFSC - USP - São Carlos - Brasil
>>
>>
>>
>> Viswanadham Sridhara wrote:
>>
>> > Did you try 1/3*your integral
>> >
>> > On 2/22/06, *Alexandre Suman de Araujo* <asaraujo at if.sc.usp.br
>> > <mailto:asaraujo at if.sc.usp.br>> wrote:
>> >
>> > Hi Gmxers.
>> >
>> > I´m trying to calculate coefficient diffusion values for ions in
>> > water.
>> >
>> > I made some calculations using MSD and the results were in good
>> > agreement with experimental values.
>> >
>> > The problem is when I try to calculate it from integration of VAC
>> > function for the ions, like in Rasaiah paper (J. Chem Phys. 101(8)
>> > 6964).
>> >
>> > I made 40 simulations of 250 ps with 1 fs time step and output of
>> > velocities every 1 fs. From these simulations I calculated the
>> > normalized VAC function from these 40 simulations and calculated the
>> > mean. This methodology is implemented to have a good statistic and a
>> > more smooth VAC function (without fluctuations that could make the
>> > integral diverge). With this VAC function I use this equation to
>> > calculate do diffusion coefficient:
>> >
>> > D = kT/M*Y, where Y is the integral of the VAC function
>> >
>> > The problem is that the value calculated from VAC does not agree
>> with
>> > one calculated from MSD.
>> >
>> > Does anyone knows any trick to perform this kind of calculation?
>> > In the
>> > paper cited above these two values are very near and I´m using the
>> > same
>> > methodology.
>> >
>> > Thank´s!
>> >
>> > --
>> > Alexandre Suman de Araujo
>> > asaraujo at if.sc.usp.br <mailto:asaraujo at if.sc.usp.br>
>> > UIN: 6194055
>> > IFSC - USP - São Carlos - Brasil
>> >
>> > _______________________________________________
>> > gmx-users mailing list gmx-users at gromacs.org
>> > <mailto:gmx-users at gromacs.org>
>> > http://www.gromacs.org/mailman/listinfo/gmx-users
>> > Please don't post (un)subscribe requests to the list. Use the
>> > www interface or send it to gmx-users-request at gromacs.org
>> > <mailto:gmx-users-request at gromacs.org>.
>> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>> > <http://www.gromacs.org/mailing_lists/users.php>
>> >
>> >
>> >
>> >
>> > --
>> > Viswanadham Sridhara,
>> > Graduate Research Assistant,
>> > Old Dominion University, "VIRGINIA".
>> >
>> >------------------------------------------------------------------------
>> >
>> >_______________________________________________
>> >gmx-users mailing list gmx-users at gromacs.org
>> >http://www.gromacs.org/mailman/listinfo/gmx-users
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>
>
>
>--
>Viswanadham Sridhara,
>Graduate Research Assistant,
>Old Dominion University, "VIRGINIA".
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>------------------------------
>
>Message: 3
>Date: Wed, 22 Feb 2006 21:07:39 +0100
>From: David van der Spoel <spoel at xray.bmc.uu.se>
>Subject: Re: [gmx-users] Re: ewald_rtol and convergence
>To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>Message-ID: <43FCC48B.4050703 at xray.bmc.uu.se>
>Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>Michael Shirts wrote:
>> So, it turns out that the problem with the poor convergence is that I
>> accidentally had pbc = no set instead of pbx = xyz in the mdp. Once
>> that was fixed, covergence was much more reasonable.
>>
>> I'm wondering if there should be a warning in the code that says "Do
>> you REALLY want to use Ewald with a non-periodic system?"
>>
>Done.
>
>> Thanks,
>> Michael
>>
>> On 2/17/06, Michael Shirts <mrshirts at gmail.com> wrote:
>>
>>>Hi, all-
>>>
>>>So, I'm wondering what the effect of ewald_rtol is. My understanding
>>>is that it should just be shifting the calculation between the real
>>>space and the reciprocal space summations. But the total
>>>electrostatic is changing non-negligibly as well. My system is a box
>>>of waters with a protein -- total charge is zero. PME Cutoff is 0.9,
>>>fourier_spacing is 0.02 (so well converged in all cases), PME order 6.
>>>Octahedral box, (5.78643,5.45550,4.72461) box vector, all the same
>>>configuration.
>>>
>>>Ewald_rtol total Short range
>>> Long range 1/beta (nm)
>>>1e-02 -53195.725708 -46946.948640 -6248.777068
>>> 0.494129
>>>1e-03 -53432.220675 -45014.961538 -8417.259138
>>> 0.386805
>>>1e-04 -53652.773007 -43093.541701 -10559.231306
>>> 0.327146
>>>1e-05 -53872.777698 -41119.255332 -12753.522366
>>> 0.288146
>>>1e-06 -54092.976378 -39070.390423 -15022.585955
>>> 0.260198
>>>
>>>I did some comparison to straight Ewald, as well.
>>>
>>>Ewald_rtol total Short range
>>> Long range
>>>1e-02 -52899.579997 -46946.948640 -5952.631357
>>>1e-03 -53001.090875 -45014.961538 -7986.129337
>>>1e-05 -53182.993892 -41119.255332 -12063.738560
>>>
>>>We see that the short range part is exactly the same in PME and
>>>straight Ewald, as it should, though the long range part is not the
>>>same, even when the PME part is well converged (i.e., I reduced the
>>>fourier_spacing until any changes were sub 0.002 kJ/mol, which is one
>>>part in 25 million).
>>>
>>>I'm unsure why the differences. It there coding issue with the
>>>octahedral box? Is there some effect with the dielectic at infinity
>>>(i'm using epsilon_surface = 0). What is the 'true' electrostatic
>>>energy?
>>>I tried different cutoffs -- presumably, as we take a low rtol,
>>>pushing the calculation further into the direct space, and choose a
>>>longer cutoff, the correction will get more accurate.
>>>
>>>PME: (order 6, ewald_rtol = 1e-02)
>>>cutoff total Short range
>>>Long range 1/beta
>>>
>>>0.9 -53195.725708 -46946.948640 -6248.777068
>>> 0.494129
>>>1.8 -52875.688467 -49910.307947 -2965.380520
>>> 0.988258
>>>2.7 -52798.032604 -50836.767614 -1961.264991
>>> 1.48239
>>>3.6 -52764.124490 -51296.887618 -1467.236872
>>> 1.97652
>>>4.5 -52745.340510 -51572.825196 -1172.515314
>>> 2.47065
>>>
>>>Ewald: (fourier_nx,ny,nz = 25)
>>>
>>>0.9 -52899.579997 -46946.948640 -5952.631357
>>> 0.494129
>>>1.8 -52785.799065 -49910.307947 -2875.491118
>>> 0.988258
>>>2.7 -52761.626727 -50836.767614 -1924.859113
>>> 1.48239
>>>3.6 -52747.927053 -51296.887618 -1451.039435
>>> 1.97652
>>>4.5 -52738.223387 -51572.825196 -1165.398191
>>> 2.47065
>>>
>>>So it seems that -52730 is closer to the "right" answer. Why isn't
>>>this more possible to with other combinations of terms? Am I missing
>>>something? Is this level of agreement (both for Ewald, and between
>>>PME and Ewald) an unreasonable expectation? :)
>>>
>>>Thanks,
>>>Michael
>>>
>>
>> _______________________________________________
>> gmx-users mailing list gmx-users at gromacs.org
>> http://www.gromacs.org/mailman/listinfo/gmx-users
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
>
>--
>David.
>________________________________________________________________________
>David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
>Dept. of Cell and Molecular Biology, Uppsala University.
>Husargatan 3, Box 596, 75124 Uppsala, Sweden
>phone: 46 18 471 4205 fax: 46 18 511 755
>spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>
>
>------------------------------
>
>Message: 4
>Date: Wed, 22 Feb 2006 17:37:59 +0000
>From: Alexandre Suman de Araujo <asaraujo at if.sc.usp.br>
>Subject: Re: [gmx-users] Diffusion Coefficient from VAC
>To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>Message-ID: <43FCA177.2070807 at if.sc.usp.br>
>Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>I mean that from MSD I have a value of 1.5 cm^2/s and from VAC 0.9
>cm^2/s. The experimental value is 1.9 cm^2/s.
>In the paper I cited, they had values from VAC and MSD differing in 0.1
>cm^2/s in some cases.
>
>Alexandre Suman de Araujo
>asaraujo at if.sc.usp.br
>UIN: 6194055
>IFSC - USP - São Carlos - Brasil
>
>
>
>Frederic Leroy wrote:
>
>> What do you mean quantatively by "VAC does not agree with one
>> calculated from MSD"?
>>
>>
>>
>> Alexandre Suman de Araujo wrote:
>>
>>> Hi Gmxers.
>>>
>>> I´m trying to calculate coefficient diffusion values for ions in water.
>>>
>>> I made some calculations using MSD and the results were in good
>>> agreement with experimental values.
>>>
>>> The problem is when I try to calculate it from integration of VAC
>>> function for the ions, like in Rasaiah paper (J. Chem Phys. 101(8)
>>> 6964).
>>>
>>> I made 40 simulations of 250 ps with 1 fs time step and output of
>>> velocities every 1 fs. From these simulations I calculated the
>>> normalized VAC function from these 40 simulations and calculated the
>>> mean. This methodology is implemented to have a good statistic and a
>>> more smooth VAC function (without fluctuations that could make the
>>> integral diverge). With this VAC function I use this equation to
>>> calculate do diffusion coefficient:
>>>
>>> D = kT/M*Y, where Y is the integral of the VAC function
>>>
>>> The problem is that the value calculated from VAC does not agree with
>>> one calculated from MSD.
>>>
>>> Does anyone knows any trick to perform this kind of calculation? In
>>> the paper cited above these two values are very near and I´m using
>>> the same methodology.
>>>
>>> Thank´s!
>>>
>>
>> _______________________________________________
>> gmx-users mailing list gmx-users at gromacs.org
>> http://www.gromacs.org/mailman/listinfo/gmx-users
>> Please don't post (un)subscribe requests to the list. Use the www
>> interface or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
>
>
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>
>End of gmx-users Digest, Vol 22, Issue 91
>*****************************************
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