[gmx-users] Diffusion coefficient water
Justin Lemkul
jalemkul at vt.edu
Thu Aug 18 14:23:15 CEST 2016
On 8/18/16 6:48 AM, Diez Fernandez, Amanda wrote:
> 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?
>
Yes, averaging over multiple, independent simulations is the correct approach.
> 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?
>
DispCorr = EnerPres is correct. If you're having trouble reproducing a
published result, you should ask the authors of the study for their advice.
-Justin
> 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
>> 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.
>>
>> End of gromacs.org_gmx-users Digest, Vol 148, Issue 68
>> ******************************************************
>
--
==================================================
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
==================================================
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