[AMBER] CPPTRAJ: Time Correlation Function (TCF)

From: emanuele falbo <falbo.emanuele.gmail.com>
Date: Mon, 29 Jun 2020 14:26:06 +0100

Dear all,

I am trying to extract the time correlation function (TCF) of a bond
vector, i.e. distance between two residues, from the MD by using cpptraj.
However, since it is the first time I am dealing with this variable, I
wanted some clarifications about the command options.
The way I obtain the TCF is the following in cpptraj:

>parm file.prmtop
>trajin file.nc
>vector v1 .454 .902
>timecorr vec1 v1 tstep 1 tcorr 100.0 out test.out order 2 norm

I noticed that using a smaller time step (tstep=1, 0.002) gives a TCF
which decays to lower values. For example, when tstep=1 (default) TCF
ranges between 1-0.95, whereas when tstep=0.002 TCF is within 1-0.3,
provided tcorr is the same( for example tcorr=100)

So, does tstep need to equal to the one used in the MD to have the
correct TCF ?

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 ?

Best Regards,

*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 Mon Jun 29 2020 - 06:30:06 PDT
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