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

From: emanuele falbo <falbo.emanuele.gmail.com>
Date: Wed, 15 Jul 2020 15:29:40 +0100

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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-- 
*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 Wed Jul 15 2020 - 08:00:04 PDT
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