Re: [AMBER] CPPTRAJ: Time Correlation Function (TCF)

From: emanuele falbo <falbo.emanuele.gmail.com>
Date: Thu, 16 Jul 2020 09:55:57 +0100

Dear Souvik,

Thanks for clarifying, however, I still have some doubts about the relative
time parameters.
For example, when loading the MD trajectory (5000 frames of 21000 ps MD
with dt=0.002ps), and changing tcorr to,
 for example, 21000 (ps) with tstep=0.002, it still gives the same results
as if tcorr= 100 (ps) and tstep=0.002 (ps) were being used:
It is like the tcorr parameter is ignored at all.

Cheers,
Manuele

Il giorno mer 15 lug 2020 alle ore 17:06 Souvik <sdey8.uic.edu> ha scritto:

>
> Dear Emanuele,
>
>
> Tstep is how often you save your trajectory. Your simulation timestep is
> 0.002 ps but did you save every frame and did not skip anything? Also,
> tcorr
> is the limit upto which you wish to calculate the correlation function
> in
> ps. So, when you use tcorr to be 100, you would only calculate it upto
> 100
> ps whereas you have a trajectory of 21000 ps.
>
>
> Cheers,
>
> Souvik
>
>
> Sent from [1]Mail for Windows 10
>
>
> From: [2]emanuele falbo
> Sent: Wednesday, July 15, 2020 9:30 AM
> To: [3]AMBER Mailing List
> Subject: Re: [AMBER] CPPTRAJ: Time Correlation Function (TCF)
>
>
> Dear Daniel,
>
>
> Thanks for the heads-up, however, I decided to only focus on relevant
>
> ligands and
>
> not to use the loops. That said, I managed to get the TCF, however, I am
>
> having another type of issues:
>
> essentially, the time in output of "timecorr" doesn't correspond to the
>
> full time of the dynamics.
>
>
> For example, I run a 21000 ps MD with tstep=0.002, and from the
> following
>
> commands
>
>
> >parm ../../topology.prmtop
>
> >trajin .././trajectory.mdcrd
>
> >vector v1 .536 @700
>
> >timecorr vec1 v1 tstep 0.002 tcorr 100.0 out p-p_1.dat order 2
>
> >run
>
>
> the time variable in the file p-p_1.dat goes from 0-to-9.9980 and not to
>
> 20.0.
>
> ote, I also tried to change tcorr, but the results is the same.
>
> Do you have any idea of what's being wrong here ? Thanks.
>
>
> Cheers,
>
> Manuele
>
>
> Il giorno lun 29 giu 2020 alle ore 16:16 Daniel Roe <
> daniel.r.roe.gmail.com>
>
> ha scritto:
>
>
> > Hi,
>
> >
>
> > On Mon, Jun 29, 2020 at 9:26 AM emanuele falbo <
> falbo.emanuele.gmail.com>
>
> > wrote:
>
> > >
>
> > > So, does tstep need to equal to the one used in the MD to have the
>
> > > correct TCF ?
>
> >
>
> > Yes.
>
> >
>
> > >
>
> > > Secondly, If one wants the full TCF for the distance between two
> oxygens
>
> > > with respectively atom type O1 and O2, does the command " vector
> v1
>
> > > .%O1 @%O2" give the desired quantity ?
>
> >
>
> > No, that will use the center of mass of all atoms of type O1 to the
>
> > center of mass of all atoms of type O2. If you want every type O1 to
>
> > every type O2, you'll have to use the 'multivector' analysis command
>
> > or use a 'for X inmask' style loop.
>
> >
>
> > -Dan
>
> >
>
> > >
>
> > > Best Regards,
>
> > > Manuele
>
> > >
>
> > > --
>
> > >
>
> > > *Emanuele Falbo*
>
> > > PhD student
>
> > > Penfold group
>
> > > School of Natural and Environmental Sciences
>
> > > Bedson Building, Newcastle University
>
> > > Newcastle upon Tyne, NE1 7RU
>
> > > w: http://tompenfoldresearch.weebly.com/
>
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>
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>
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>
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>
> >
>
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>
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> >
>
>
>
> --
>
>
> *Emanuele Falbo*
>
> PhD student
>
> Penfold group
>
> School of Natural and Environmental Sciences
>
> Bedson Building, Newcastle University
>
> Newcastle upon Tyne, NE1 7RU
>
> w: http://tompenfoldresearch.weebly.com/
>
> _______________________________________________
>
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>
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>
> References
>
> 1. https://go.microsoft.com/fwlink/?LinkId=550986
> 2. mailto:falbo.emanuele.gmail.com
> 3. mailto:amber.ambermd.org
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-- 
*Emanuele Falbo*
PhD student
Penfold group
School of Natural and Environmental Sciences
Bedson Building, Newcastle University
Newcastle upon Tyne, NE1 7RU
w: http://tompenfoldresearch.weebly.com/
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Received on Thu Jul 16 2020 - 02:00:03 PDT
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