Re: [gmx-users] Diffusion coefficient

[Justin Lemkul]

On 9/17/17 6:05 PM, Dallas Warren wrote:

http://manual.gromacs.org/documentation/5.1/onlinehelp/selections.html

Don't know exactly how to do it myself, but there will be an option
there where you can specify the z coordinate as a way to break it up
into groups.


And herein lies the challenge.  The selections themselves will give index groups 
per frame, may vary in size, and the individual molecules themselves will likely 
occupy each slice discontinuously with respect to time.  So a lot of effort 
would have to be made to make per-molecule sub-trajectories to compute a 
diffusion coefficient for a given time frame in which the molecule continuously 
satisfies the criterion, then calculated again over another period of time if 
the molecule moves out and comes back (otherwise one would get a spurious 
contribution to the MSD if a molecule seems to jump around).  I suppose it can 
be done, but only very tediously in reassembling frames to make 
sub-trajectories, then looping over every molecule individually in doing so.


-Justin

--
==

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

303 Engel Hall
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Re: [gmx-users] Diffusion coefficient

[Dallas Warren]

http://manual.gromacs.org/documentation/5.1/onlinehelp/selections.html

Don't know exactly how to do it myself, but there will be an option
there where you can specify the z coordinate as a way to break it up
into groups.
Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.war...@monash.edu
-
When the only tool you own is a hammer, every problem begins to resemble a nail.


On 17 September 2017 at 06:05, Sohaib. Mohammed
 wrote:
> Any help!
>
> On Saturday, September 16, 2017, Sohaib. Mohammed <
> sohaibmohamme...@gmail.com> wrote:
>
>> Hey Users,
>>
>> I want to calculate the diffusion coefficient using gmx msd. I want to
>> divide the box into slices of 5 A parallel to z axis and calculate the
>> diffusion coefficient for each slice. My question is how to make these
>> slices, I've tried gmx trajconv but didn't work with me. I believe it's
>> quite simple and provided by gromacs, but I am struggling with it.
>> Appreciate any idea on how to make these slices.
>>
>> Thank you,
>>
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Re: [gmx-users] Diffusion coefficient

[Sohaib. Mohammed]

Any help!

On Saturday, September 16, 2017, Sohaib. Mohammed <
sohaibmohamme...@gmail.com> wrote:

> Hey Users,
>
> I want to calculate the diffusion coefficient using gmx msd. I want to
> divide the box into slices of 5 A parallel to z axis and calculate the
> diffusion coefficient for each slice. My question is how to make these
> slices, I've tried gmx trajconv but didn't work with me. I believe it's
> quite simple and provided by gromacs, but I am struggling with it.
> Appreciate any idea on how to make these slices.
>
> Thank you,
>
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Re: [gmx-users] Diffusion coefficient water

[Victor Rosas Garcia]

The following paper may also be interesting.

"System-size corrections for self-diffusion coefficients calculated from
molecular dynamics simulations: The case of CO2, n-alkanes, and
poly(ethylene glycol) dimethyl ether" J. Chem. Phys. 145, 074109 (2016);
http://dx.doi.org/10.1063/1.4960776


2016-08-18 8:35 GMT-05:00 Michael Shirts :

> See the following paper
> (http://pubs.acs.org/doi/abs/10.1021/ct400109a) for some examples of
> diffusion calculations in GROMACS.
>
> The finite size correction for diffusion coefficients is something
> different than the long range energy corrections. A discussion of this
> (I can't vouch for all the details, I just googled) is here:
> http://pubs.acs.org/doi/abs/10.1021/jp0756247
>
>
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Re: [gmx-users] Diffusion coefficient water

[Michael Shirts]

See the following paper
(http://pubs.acs.org/doi/abs/10.1021/ct400109a) for some examples of
diffusion calculations in GROMACS.

The finite size correction for diffusion coefficients is something
different than the long range energy corrections. A discussion of this
(I can't vouch for all the details, I just googled) is here:
http://pubs.acs.org/doi/abs/10.1021/jp0756247

On Thu, Aug 18, 2016 at 6:37 AM, Mark Abraham  wrote:
> Hi,
>
> I would also consider using a pressure-coupling algorithm that isn't known
> to create the wrong velocity distribution.
>
> Mark
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Re: [gmx-users] Diffusion coefficient water

[Mark Abraham]

Hi,

I would also consider using a pressure-coupling algorithm that isn't known
to create the wrong velocity distribution.

Mark
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Re: [gmx-users] Diffusion coefficient water

[Justin Lemkul]

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-boun...@maillist.sys.kth.se
on behalf of gromacs.org_gmx-users-requ...@maillist.sys.kth.se"
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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 <scinik...@gmail.com>
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: Re: [gmx-users] Diffusion coefficient water
Message-ID:

Re: [gmx-users] Diffusion coefficient water

[Diez Fernandez, Amanda]

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-boun...@maillist.sys.kth.se
on behalf of gromacs.org_gmx-users-requ...@maillist.sys.kth.se"
<gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of
gromacs.org_gmx-users-requ...@maillist.sys.kth.se> wrote:

>Send gromacs.org_gmx-users mailing list submissions to
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>When replying, please edit your Subject line so it is more specific
>than "Re: Contents of gromacs.org_gmx-users digest..."
>
>
>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 <scinik...@gmail.com>
>To: gromacs.org_gmx-users@maillist.sys.kth.se
>Subject: Re: [gmx-users] Diffusion coefficient water
>Message-ID:
>   

Re: [gmx-users] Diffusion coefficient water

[li he]

4. you could even try NVT ensemble

2016-08-18 2:25 GMT+08:00 li he :

> 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.die...@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!
>>
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>> send a mail to gmx-users-requ...@gromacs.org.
>>
>
>
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Re: [gmx-users] Diffusion coefficient water

[li he]

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.die...@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
> --
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Re: [gmx-users] Diffusion coefficient water

[Justin Lemkul]

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

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] Diffusion coefficient water

[Nikhil Maroli]

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
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Re: [gmx-users] Diffusion coefficient of metal complex

[Justin Lemkul]

On 7/23/14, 7:13 AM, Meena Singh wrote:

Dear GROMACS users,

I'm working on the diffusivity of metal ion with its ligand in organic
phase.

I want to calculate the diffusion coefficient of metal-ligand complex as a
group, but when I run g_msd command the option are there for only
individual molecules diffusivity calculation.

Can I calculate the diffusion coefficient of specific complex from the box
which contains metal ions and ligand molecules.

Does anyone have a suggestion to help me with this problem?



Create an index group for whatever subset of atoms you like and use it for the 
calculation.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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