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From: newamber list <newamberlist.gmail.com>

Date: Fri, 2 Jan 2015 21:24:11 +0000

Dear Daniel,

Thanks.

*>Depending on how many frames are in that 12-14 ps and how many
*

*>particles you're averaging over it could be - however fitting a line
*

*>to only 6 points seems like that's not enough data to me.
*

Mostly number of particles averaged are 50,000 to 100,000 in 20 to 50 ns

time scale (frames saved after 2 ps) in volume of approx. 400 Angstrom^3.

Is this enough? Roughly I found regular stay time of majority particles in

this volume was 14 to 20 ps. (Even the same ion lets say stay from t to t+6

ps in that volume and comes back in from t+10 to t+x ps then I count it as

two different events of stay). Thus beyond I don't expect to have a linear

relation.

*>> Sure, you have 5x less data if you're saving 1 frame every 10 ps as
*

opposed to 2 ps, but particles aren't >>going to do all that much more in

that interval at the speeds particles will travel in simulations at

*>>typical temperatures
*

Somehow I think (wrong?) diffusion calculation will depend on volume so

chosen and minimal time step as explained with this example: Assume huge

bulk water with ions simulation and you have trajectory for each 1ps then

it will not matter if you do calculation on full box with different time

steps diffusion coeff will not change. But if calculated in extremely small

volume in the bulk box itself then I think one need to reduce the time step

as well (such a extremely small volume that ion can jump within 1ps in such

case I need to save trajectory less than 1 ps time step). In summary what I

am thinking is (wrong?!) diffusion calculation will be wrong in such case

even if I average on large number of particles.

Cpptraj does MSD calculations considering initial position. Considering

this and above situation (small volume and regular time stay of 14-20ps)

lets take an example in case of every 10 ps frame saved trajectory: Lets

say at time t ion was inside small volume and the ion move out and comes

back in but I will see that it moved only a little in t+10 ps time as I

have no information of t+10 - t time scale. I will wrongly interpret it as

slow diffusion. I think is true for a case of extremely small volume even

*>> but it is important that there be no imaging in your input trajectory
*

Yes, I have taken care.

regards,

Jiom

On Fri, Jan 2, 2015 at 7:24 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:

*> Hi,
*

*>
*

*> On Fri, Jan 2, 2015 at 9:12 AM, newamber list <newamberlist.gmail.com>
*

*> wrote:
*

*> >>> It's not clear what you mean by "different temperature controls"
*

*> >
*

*> > Sorry I used the term lightly. AMBER one is with Berendsen and CHARMM
*

*> with
*

*> > langevin dynamics.
*

*>
*

*> This will certainly cause differences in diffusion rates. In fact, if
*

*> you're looking to compare to experimental values you should use no
*

*> thermostat (i.e. NVE ensemble) or an extremely weak thermostat (e.g.
*

*> Berendsen with extremely long coupling constant), combined with
*

*> tighter SHAKE tolerance and a short (1 fs) time step.
*

*>
*

*> >>> You mention "ions in some constricted space": if there are not very
*

*> many
*

*> > of these, you may have considerably difficulty in getting a converged
*

*> > result.
*

*> >
*

*> > Yes that is true. For my one case (AMBER) coordinates are saved after 2
*

*> ps
*

*> > and in this constricted volume I actually take an average over long part
*

*> of
*

*> > simulation and over all the particles. I get quite linear MSD vs time
*

*> > relation upto 12-14 ps (linear line with 6 points) from which I get
*

*> > diffusion coefficient values. Hope its fine?
*

*>
*

*> Depending on how many frames are in that 12-14 ps and how many
*

*> particles you're averaging over it could be - however fitting a line
*

*> to only 6 points seems like that's not enough data to me.
*

*>
*

*> > But in CHARMM case, someone can suggest, I have frames saved after 10 ps
*

*> > only. So problem is having less samples of particles in constricted space
*

*> > (volume) which is not reliable. Other thing is in 10 ps a particle may
*

*> > leave and enter the same volume that will be counted as regular path
*

*> which
*

*> > is wrong (single event). As particle can come inside, stay and then leave
*

*> > small volume few times in 10 ps those should be counted as different
*

*> > events. Also the particle may stay in constricted space for long (~20-30
*

*> > ps) then in this case am averaging over only slow diffusing particles
*

*> hence
*

*> > may be am getting three times lower values than AMBER case in which I can
*

*> > capture both fast and slow particles as frames are saved after 2ps. I am
*

*> > not sure if am thinking correctly.
*

*>
*

*> I feel like you may be over-thinking this a bit actually. Sure, you
*

*> have 5x less data if you're saving 1 frame every 10 ps as opposed to 2
*

*> ps, but particles aren't going to do all that much more in that
*

*> interval at the speeds particles will travel in simulations at typical
*

*> temperatures. If you have enough data and all other conditions are the
*

*> same the answers should agree well with each other. You can convince
*

*> yourself of this by re-doing your diffusion calculation on your 2 ps
*

*> data but reading only every 5th frame (e.g. in cpptraj 'trajin
*

*> mytraj.nc 1 last 5') - if you have enough sampling your results should
*

*> match.
*

*>
*

*> One important thing to keep in mind - you don't give many details
*

*> about your simulations or how you are performing the diffusion
*

*> calculation, but it is important that there be no imaging in your
*

*> input trajectory. If there is this will certainly throw off your
*

*> calculation (since when a molecule is imaged it appears to jump an
*

*> entire box length in 1 frame). You can use the cpptraj 'unwrap'
*

*> command to remove any imaging.
*

*>
*

*> Hope this helps,
*

*>
*

*> -Dan
*

*>
*

*> >
*

*> > Indeed it should not matter if we take 2ps or 10 ps time step for
*

*> > diffusion calculation if it was done on infinite bulk volume without any
*

*> > constrictions/restrictions.
*

*> >
*

*> > Thanks for your time and suggestions.
*

*> >
*

*> > regards,
*

*> > Jiom
*

*> >
*

*> >
*

*> >
*

*> > On Fri, Jan 2, 2015 at 1:10 PM, David A Case <case.biomaps.rutgers.edu>
*

*> > wrote:
*

*> >
*

*> >> On Thu, Jan 01, 2015, newamber list wrote:
*

*> >> >
*

*> >> > I have question related to diffusion time step that we define in
*

*> cpptraj
*

*> >> > 'diffusion' calculation. Query divided in two parts:
*

*> >> >
*

*> >> > 1) I have trajectory coordinates saved after 2ps, thus in cpptraj I
*

*> will
*

*> >> > define time_per_frame as 2. But if same trajectory is used with frames
*

*> >> > stripped and saved after 10 ps and using time_per_frame as 10 then
*

*> >> should I
*

*> >> > expect nearly same diffusion coeff. values?
*

*> >>
*

*> >> Yes.
*

*> >>
*

*> >> >
*

*> >> > 2) Actually I have some complex situation and I have number of
*

*> >> variables. I
*

*> >> > have one simulation with AMBER ff and other with CHARMM and time
*

*> frames
*

*> >> > saved after 2 and 10 ps respectively that too with different
*

*> temperature
*

*> >> > controls. I am getting three times difference in the diffusion values
*

*> for
*

*> >> > ions in some constricted space of interest. I am not sure whether I
*

*> >> should
*

*> >> > expect the differences or not. If yes then such (three times)
*

*> difference
*

*> >> is
*

*> >> > acceptable?
*

*> >> >
*

*> >>
*

*> >> It's not clear what you mean by "different temperature controls".
*

*> >> Diffusion
*

*> >> constants are strongly dependent upon temperature, and also upon the
*

*> force
*

*> >> field. (In particular, TIP3P water is dramatically different from most
*

*> >> other
*

*> >> popular water models; this may also influence ionic diffusion.
*

*> >>
*

*> >> Be sure that you are not just looking at anectodal evidence. You
*

*> mention
*

*> >> "ions in some constricted space": if there are not very many of these,
*

*> you
*

*> >> may have considerably difficulty in getting a converged result.
*

*> >>
*

*> >> ....dac
*

*> >>
*

*> >>
*

*> >> _______________________________________________
*

*> >> AMBER mailing list
*

*> >> AMBER.ambermd.org
*

*> >> http://lists.ambermd.org/mailman/listinfo/amber
*

*> >>
*

*> > _______________________________________________
*

*> > AMBER mailing list
*

*> > AMBER.ambermd.org
*

*> > http://lists.ambermd.org/mailman/listinfo/amber
*

*>
*

*>
*

*>
*

*> --
*

*> -------------------------
*

*> Daniel R. Roe, PhD
*

*> Department of Medicinal Chemistry
*

*> University of Utah
*

*> 30 South 2000 East, Room 307
*

*> Salt Lake City, UT 84112-5820
*

*> http://home.chpc.utah.edu/~cheatham/
*

*> (801) 587-9652
*

*> (801) 585-6208 (Fax)
*

*>
*

*> _______________________________________________
*

*> AMBER mailing list
*

*> AMBER.ambermd.org
*

*> http://lists.ambermd.org/mailman/listinfo/amber
*

*>
*

_______________________________________________

AMBER mailing list

AMBER.ambermd.org

http://lists.ambermd.org/mailman/listinfo/amber

Received on Fri Jan 02 2015 - 13:30:03 PST

Date: Fri, 2 Jan 2015 21:24:11 +0000

Dear Daniel,

Thanks.

Mostly number of particles averaged are 50,000 to 100,000 in 20 to 50 ns

time scale (frames saved after 2 ps) in volume of approx. 400 Angstrom^3.

Is this enough? Roughly I found regular stay time of majority particles in

this volume was 14 to 20 ps. (Even the same ion lets say stay from t to t+6

ps in that volume and comes back in from t+10 to t+x ps then I count it as

two different events of stay). Thus beyond I don't expect to have a linear

relation.

opposed to 2 ps, but particles aren't >>going to do all that much more in

that interval at the speeds particles will travel in simulations at

Somehow I think (wrong?) diffusion calculation will depend on volume so

chosen and minimal time step as explained with this example: Assume huge

bulk water with ions simulation and you have trajectory for each 1ps then

it will not matter if you do calculation on full box with different time

steps diffusion coeff will not change. But if calculated in extremely small

volume in the bulk box itself then I think one need to reduce the time step

as well (such a extremely small volume that ion can jump within 1ps in such

case I need to save trajectory less than 1 ps time step). In summary what I

am thinking is (wrong?!) diffusion calculation will be wrong in such case

even if I average on large number of particles.

Cpptraj does MSD calculations considering initial position. Considering

this and above situation (small volume and regular time stay of 14-20ps)

lets take an example in case of every 10 ps frame saved trajectory: Lets

say at time t ion was inside small volume and the ion move out and comes

back in but I will see that it moved only a little in t+10 ps time as I

have no information of t+10 - t time scale. I will wrongly interpret it as

slow diffusion. I think is true for a case of extremely small volume even

Yes, I have taken care.

regards,

Jiom

On Fri, Jan 2, 2015 at 7:24 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:

_______________________________________________

AMBER mailing list

AMBER.ambermd.org

http://lists.ambermd.org/mailman/listinfo/amber

Received on Fri Jan 02 2015 - 13:30:03 PST

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