Hi,
You don’t want to use velocity as coordinates here - temperature is a
function of velocity, so cpptraj expects velocities. Use ‘trajin traj.nc
mdvel md.mdvlc’ to read in coordinates from traj.nc and velocities from
md.mdvlc.
Cpptraj should kick back at least a warning if velocities arent present for
temperature. If it doesn't I need to fix that.
-Dan
On Sat, Sep 1, 2018 at 4:35 AM Ikuo KURISAKI <kurisaki.bear.kobe-u.ac.jp>
wrote:
>
> Dear Ambers,
>
> Thanks you for usual supports,
> I'd like to beg your help again.
>
>
> I'm now trying to calculate solute temperature with velocity file by
> employing cpptraj in Amber 17.
>
> However, each temperature value was 0.000, thus possibly being not treated.
>
> ---------------------------------------------------------------------
> #Frame t1
> 1 0.0000
> 2 0.0000
> 3 0.0000
> .
> .
> .
> ---------------------------------------------------------------------
>
> Then I'm most glad if you point the failure of my input shown below.
> ---------------------------------------------------------------------
> trajin md.mdvlc usevelascoords (<=== mdvlc file is formatted in
> NetCDF.)
> rms first .CA out check.csv (<=== This is given to check
> whether
> mdvlc is read)
> temperature t1 @1-1361 ntc 2 out temp.csv (<=== NTC is set to 2 in MD
> simulation)
> ---------------------------------------------------------------------
>
> I found the 'rms' works well.
> There is a problem on 'temperature' command line, I'm guessing...
>
> Best regards,
>
>
> Kurisaki
>
>
>
>
>
>
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>
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Received on Sat Sep 01 2018 - 06:00:02 PDT
