[gmx-users] Diffusion coefficient water
Diez Fernandez, Amanda
amanda.diez10 at imperial.ac.uk
Thu Aug 18 12:48:39 CEST 2016
Thanks Justin and Nikhil,
1) So in principle is it expected that results will be different and I
should take my final value to be the average of, say, 10 simulations?
2)If so, the average over my simulations is not similar to the published
average. They also use a unit cell of 216 molecules (I use 221 molecules).
They have "long-range corrections for both the energy and pressure². Is
this equivalent to DispCorr = EnerPres ? What other
corrections should I do?
Thanks,
Amanda
On 17/08/2016, 19:28, "gromacs.org_gmx-users-bounces at maillist.sys.kth.se
on behalf of gromacs.org_gmx-users-request at maillist.sys.kth.se"
<gromacs.org_gmx-users-bounces at maillist.sys.kth.se on behalf of
gromacs.org_gmx-users-request at maillist.sys.kth.se> wrote:
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>Today's Topics:
>
> 1. Re: Diffusion coefficient water (Nikhil Maroli)
> 2. Re: Diffusion coefficient water (Justin Lemkul)
> 3. is there martini CG parameters for K+ ion? (li he)
> 4. Re: Diffusion coefficient water (li he)
> 5. Fwd: is there martini CG parameters for K+ ion? (li he)
> 6. Re: Diffusion coefficient water (li he)
>
>
>----------------------------------------------------------------------
>
>Message: 1
>Date: Wed, 17 Aug 2016 21:49:45 +0530
>From: Nikhil Maroli <scinikhil at gmail.com>
>To: gromacs.org_gmx-users at maillist.sys.kth.se
>Subject: Re: [gmx-users] Diffusion coefficient water
>Message-ID:
> <CAMEzy6QX0q5dF94ykgOckdtvZxZwpwpsY6-=BU1w2K160FFpFw at mail.gmail.com>
>Content-Type: text/plain; charset=UTF-8
>
>I don't think we can reproduce the exact results in MD .The overall
>behaviour of the system will be same .so it's obvious
>
>
>------------------------------
>
>Message: 2
>Date: Wed, 17 Aug 2016 13:11:02 -0400
>From: Justin Lemkul <jalemkul at vt.edu>
>To: gmx-users at gromacs.org
>Subject: Re: [gmx-users] Diffusion coefficient water
>Message-ID: <8eb7b1ee-041c-906d-f7a1-7e6d683c4bf2 at vt.edu>
>Content-Type: text/plain; charset=windows-1252; format=flowed
>
>
>
>On 8/17/16 11:28 AM, Diez Fernandez, Amanda wrote:
>> Dear Gromacs users,
>>
>> I was trying to reproduce the published values for the diffusion
>>coefficient of SPCFw water (2.3 +/- 0.08 x 10^-9 m^2/s )before using it
>>in some of my simulations and I am failing to do so.
>> More worryingly I get different results for different identical runs.
>> I am using a 2nm side cubic cell containing 221 water molecules and a
>>time step of 0.5fs (larger timestep results in a warning since I am not
>>applying any constraints).
>> I ran 6 identical simulations (only difference is the random initial
>>velocities) and I got these different values and error magnitudes.
>> The trajectories are 10ns long. I discarded the first 2ns for the msd
>>calculation.
>>
>> Nth Simulation Diffusion Coefficient (x 10^-9 m^2/s)
>>
>> 1 2.95 +/- 0.071
>> 2 2.71 +/- 0.158
>> 3 2.52 +/- 0.007
>> 4 2.96 +/- 0.26
>> 5 2.62 +/- 0.07
>> 6 2.71 +/- 0.158
>>
>> Is it normal that I get different results like this? (Despite
>>averaging over more than 7ns and 221 molecules?).
>>
>
>Diffusion constants are subject to finite-size effects. Have you
>corrected for
>this phenomenon? And perhaps more importantly, did the original authors
>of the
>water model correct their values? I find that often times people don't,
>or
>otherwise don't say if the correction has been applied. 2 nm is a very
>small
>box, so the PBC correction will be quite substantial.
>
>-Justin
>
>> Many thanks in advance. Below are the detailed parameters.
>>
>> Amanda
>>
>> Detailed parameters:
>>
>> nstlist = 10
>>
>> ns_type = grid
>>
>> rlist = 0.9
>>
>> coulombtype = PME
>>
>> rcoulomb = 0.9
>>
>> fourierspacing = 0.12
>>
>> pme_order = 4
>>
>> ewald_rtol = 1e-6
>>
>> vdw-type = cut-off
>>
>> rvdw = 0.9
>>
>> pbc = xyz
>>
>> tcoupl = nose-hoover
>>
>> tc_grps = SYSTEM
>>
>> tau_t = 0.4
>>
>> ref_t = 298
>>
>> nsttcouple =-1
>>
>> nh-chain-length = 1
>>
>> pcoupl = Berendsen
>>
>> pcoupltype = isotropic
>>
>> tau_p = 10.0
>>
>> compressibility = 4.5e-5
>>
>> ref_p = 1.01325
>>
>> refcoord-scaling = all
>>
>> DispCorr = EnerPres
>>
>> gen_vel = yes
>>
>> gen_temp = 293
>>
>> gen_seed = -1
>>
>> constraints = none
>>
>
>--
>==================================================
>
>Justin A. Lemkul, Ph.D.
>Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
>Department of Pharmaceutical Sciences
>School of Pharmacy
>Health Sciences Facility II, Room 629
>University of Maryland, Baltimore
>20 Penn St.
>Baltimore, MD 21201
>
>jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>http://mackerell.umaryland.edu/~jalemkul
>
>==================================================
>
>
>------------------------------
>
>Message: 3
>Date: Thu, 18 Aug 2016 02:17:28 +0800
>From: li he <parachuternewyork at gmail.com>
>To: gromacs.org_gmx-users at maillist.sys.kth.se
>Subject: [gmx-users] is there martini CG parameters for K+ ion?
>Message-ID:
> <CAGRCqu7aYE6JsD_1mByyKodQOM-HtFUKAKK7Xn5NnjV_mUcejA at mail.gmail.com>
>Content-Type: text/plain; charset=UTF-8
>
>Dear gmxers,
>I am not sure if I'd better post my question here, but the martini forum
>http://www.cgmartini.nl/index.php/forum does not allow me register and
>post my
>question there.
>I am trying to simulate some KCl solution, but only find martini CG Na+
>parameters
>at http://cgmartini.nl/images/parameters/ITP/martini_v2.0_ions.itp
>I am wondering where I can find martini parameters for K+ ion, or can I
>just use martini
>Na+ parameters for K+?
>If there is a martini parameter of K+, I could image it should be Qd bead
>with +1 charge, exactly the same as Na+ parameters at the above link. Yes,
>it is upsetting to use the same parameter for Na+ and K+, but we have to
>admit the current martini force field is not very fine tuned, thus have to
>just use Na+ martini parameters at the above link for K+ if we want to
>simulate CG KCl or martini KCl anyway? Can this way be justified if the
>simulation results agree with the results of other studies, either
>experiments or simulations?
>Thanks a lot for your kind help, and any suggestion or comment is very
>welcome.
>Yours
>he li
>
>
>------------------------------
>
>Message: 4
>Date: Thu, 18 Aug 2016 02:25:09 +0800
>From: li he <parachuternewyork at gmail.com>
>To: gmx-users at gromacs.org
>Subject: Re: [gmx-users] Diffusion coefficient water
>Message-ID:
> <CAGRCqu74vaoaBSoFZjr67PNiFQC3BdJES7xo0UMf96zE3kV8rg at mail.gmail.com>
>Content-Type: text/plain; charset=UTF-8
>
>I think you could try following things to see if you could get 'better'
>results
>1. use time step of 0.2 or even 0.1 fs
>2. try different tau-t and tau-p, e.g. use larger tau-t
>3. try different p-coupling methods
>
>2016-08-17 23:28 GMT+08:00 Diez Fernandez, Amanda <
>amanda.diez10 at imperial.ac.uk>:
>
>> Dear Gromacs users,
>>
>> I was trying to reproduce the published values for the diffusion
>> coefficient of SPCFw water (2.3 +/- 0.08 x 10^-9 m^2/s )before using
>>it in
>> some of my simulations and I am failing to do so.
>> More worryingly I get different results for different identical runs.
>> I am using a 2nm side cubic cell containing 221 water molecules and a
>>time
>> step of 0.5fs (larger timestep results in a warning since I am not
>>applying
>> any constraints).
>> I ran 6 identical simulations (only difference is the random initial
>> velocities) and I got these different values and error magnitudes.
>> The trajectories are 10ns long. I discarded the first 2ns for the msd
>> calculation.
>>
>> Nth Simulation Diffusion Coefficient (x 10^-9 m^2/s)
>>
>> 1 2.95 +/- 0.071
>> 2 2.71 +/- 0.158
>> 3 2.52 +/- 0.007
>> 4 2.96 +/- 0.26
>> 5 2.62 +/- 0.07
>> 6 2.71 +/- 0.158
>>
>> Is it normal that I get different results like this? (Despite averaging
>> over more than 7ns and 221 molecules?).
>>
>> Many thanks in advance. Below are the detailed parameters.
>>
>> Amanda
>>
>> Detailed parameters:
>>
>> nstlist = 10
>>
>> ns_type = grid
>>
>> rlist = 0.9
>>
>> coulombtype = PME
>>
>> rcoulomb = 0.9
>>
>> fourierspacing = 0.12
>>
>> pme_order = 4
>>
>> ewald_rtol = 1e-6
>>
>> vdw-type = cut-off
>>
>> rvdw = 0.9
>>
>> pbc = xyz
>>
>> tcoupl = nose-hoover
>>
>> tc_grps = SYSTEM
>>
>> tau_t = 0.4
>>
>> ref_t = 298
>>
>> nsttcouple =-1
>>
>> nh-chain-length = 1
>>
>> pcoupl = Berendsen
>>
>> pcoupltype = isotropic
>>
>> tau_p = 10.0
>>
>> compressibility = 4.5e-5
>>
>> ref_p = 1.01325
>>
>> refcoord-scaling = all
>>
>> DispCorr = EnerPres
>>
>> gen_vel = yes
>>
>> gen_temp = 293
>>
>> gen_seed = -1
>>
>> constraints = none
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at http://www.gromacs.org/
>> Support/Mailing_Lists/GMX-Users_List before posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-request at gromacs.org.
>>
>
>
>------------------------------
>
>Message: 5
>Date: Thu, 18 Aug 2016 02:26:37 +0800
>From: li he <parachuternewyork at gmail.com>
>To: gmx-users at gromacs.org
>Subject: [gmx-users] Fwd: is there martini CG parameters for K+ ion?
>Message-ID:
> <CAGRCqu5wyLvrnkibCfHVyoMTqoMNOmxwzEF-W1hcgoJepnz0iw at mail.gmail.com>
>Content-Type: text/plain; charset=UTF-8
>
>Dear gmxers,
>I am not sure if I'd better post my question here, but the martini forum
>http://www.cgmartini.nl/index.php/forum does not allow me register and
>post my
>question there.
>I am trying to simulate some KCl solution, but only find martini CG Na+
>parameters
>at http://cgmartini.nl/images/parameters/ITP/martini_v2.0_ions.itp
>I am wondering where I can find martini parameters for K+ ion, or can I
>just use martini
>Na+ parameters for K+?
>If there is a martini parameter of K+, I could image it should be Qd bead
>with +1 charge, exactly the same as Na+ parameters at the above link. Yes,
>it is upsetting to use the same parameter for Na+ and K+, but we have to
>admit the current martini force field is not very fine tuned, thus have to
>just use Na+ martini parameters at the above link for K+ if we want to
>simulate CG KCl or martini KCl anyway? Can this way be justified if the
>simulation results agree with the results of other studies, either
>experiments or simulations?
>Thanks a lot for your kind help, and any suggestion or comment is very
>welcome.
>Yours
>he li
>
>
>------------------------------
>
>Message: 6
>Date: Thu, 18 Aug 2016 02:27:58 +0800
>From: li he <parachuternewyork at gmail.com>
>To: gmx-users at gromacs.org
>Subject: Re: [gmx-users] Diffusion coefficient water
>Message-ID:
> <CAGRCqu577udFGywjmaXRoBAjsuLn3d6Wo_uhiy83ti1Zt1MioQ at mail.gmail.com>
>Content-Type: text/plain; charset=UTF-8
>
>4. you could even try NVT ensemble
>
>2016-08-18 2:25 GMT+08:00 li he <parachuternewyork at gmail.com>:
>
>> I think you could try following things to see if you could get 'better'
>> results
>> 1. use time step of 0.2 or even 0.1 fs
>> 2. try different tau-t and tau-p, e.g. use larger tau-t
>> 3. try different p-coupling methods
>>
>> 2016-08-17 23:28 GMT+08:00 Diez Fernandez, Amanda <
>> amanda.diez10 at imperial.ac.uk>:
>>
>>> Dear Gromacs users,
>>>
>>> I was trying to reproduce the published values for the diffusion
>>> coefficient of SPCFw water (2.3 +/- 0.08 x 10^-9 m^2/s )before using
>>>it in
>>> some of my simulations and I am failing to do so.
>>> More worryingly I get different results for different identical runs.
>>> I am using a 2nm side cubic cell containing 221 water molecules and a
>>> time step of 0.5fs (larger timestep results in a warning since I am not
>>> applying any constraints).
>>> I ran 6 identical simulations (only difference is the random initial
>>> velocities) and I got these different values and error magnitudes.
>>> The trajectories are 10ns long. I discarded the first 2ns for the msd
>>> calculation.
>>>
>>> Nth Simulation Diffusion Coefficient (x 10^-9 m^2/s)
>>>
>>> 1 2.95 +/- 0.071
>>> 2 2.71 +/- 0.158
>>> 3 2.52 +/- 0.007
>>> 4 2.96 +/- 0.26
>>> 5 2.62 +/- 0.07
>>> 6 2.71 +/- 0.158
>>>
>>> Is it normal that I get different results like this? (Despite
>>>averaging
>>> over more than 7ns and 221 molecules?).
>>>
>>> Many thanks in advance. Below are the detailed parameters.
>>>
>>> Amanda
>>>
>>> Detailed parameters:
>>>
>>> nstlist = 10
>>>
>>> ns_type = grid
>>>
>>> rlist = 0.9
>>>
>>> coulombtype = PME
>>>
>>> rcoulomb = 0.9
>>>
>>> fourierspacing = 0.12
>>>
>>> pme_order = 4
>>>
>>> ewald_rtol = 1e-6
>>>
>>> vdw-type = cut-off
>>>
>>> rvdw = 0.9
>>>
>>> pbc = xyz
>>>
>>> tcoupl = nose-hoover
>>>
>>> tc_grps = SYSTEM
>>>
>>> tau_t = 0.4
>>>
>>> ref_t = 298
>>>
>>> nsttcouple =-1
>>>
>>> nh-chain-length = 1
>>>
>>> pcoupl = Berendsen
>>>
>>> pcoupltype = isotropic
>>>
>>> tau_p = 10.0
>>>
>>> compressibility = 4.5e-5
>>>
>>> ref_p = 1.01325
>>>
>>> refcoord-scaling = all
>>>
>>> DispCorr = EnerPres
>>>
>>> gen_vel = yes
>>>
>>> gen_temp = 293
>>>
>>> gen_seed = -1
>>>
>>> constraints = none
>>> --
>>> Gromacs Users mailing list
>>>
>>> * Please search the archive at http://www.gromacs.org/Support
>>> /Mailing_Lists/GMX-Users_List before posting!
>>>
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>> * For (un)subscribe requests visit
>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>> send a mail to gmx-users-request at gromacs.org.
>>>
>>
>>
>
>
>------------------------------
>
>--
>Gromacs Users mailing list
>
>* Please search the archive at
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>
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