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

From: Daniel Roe <daniel.r.roe.gmail.com>
Date: Mon, 20 Jul 2020 10:54:56 -0400

Hi,

The 'tstep' keyword is the time between snapshots, *not* the
simulation time step. Also, tstep and tcorr should be given in the
same units. So if you were writing a trajectory frame every 1 ps, you
would provide 'tstep 1.0', if every 10 ps it would be 'tstep 10.0',
etc.

Hope this helps,

-Dan

On Thu, Jul 16, 2020 at 4:56 AM emanuele falbo <falbo.emanuele.gmail.com> wrote:
>
> 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/
> >
> > > > _______________________________________________
> >
> > > > 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
> >
> > >
> >
> >
> >
> > --
> >
> >
> > *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/
> >
> > _______________________________________________
> >
> > AMBER mailing list
> >
> > AMBER.ambermd.org
> >
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> > References
> >
> > 1. https://go.microsoft.com/fwlink/?LinkId=550986
> > 2. mailto:falbo.emanuele.gmail.com
> > 3. mailto:amber.ambermd.org
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
> --
>
> *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/
> _______________________________________________
> 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 Mon Jul 20 2020 - 08:00:05 PDT
Custom Search