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

From: Souvik <sdey8.uic.edu>
Date: Wed, 15 Jul 2020 11:06:15 -0500

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

>

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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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References

   1. https://go.microsoft.com/fwlink/?LinkId=550986
   2. mailto:falbo.emanuele.gmail.com
   3. mailto:amber.ambermd.org
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Received on Wed Jul 15 2020 - 09:30:03 PDT
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