[AMBER] Amber 16/cpptraj diffusion command

From: Pau Mayorga Delgado <Pau.MayorgaDelgado.student.oulu.fi>
Date: Mon, 25 Jan 2021 08:37:48 +0000

Dear amber group,

Is there any issue with the diffusion command in cpptraj amber-16? For a 66-lipid micelle we get a plateau value that does not follow a linear relationship and we have not seen this in other systems. There seems not to be a drift in the electrostatic interactions. This is a NVT simulation.

The commands in ptraj are as follows:

trajin Simu1_run1.mdcrd 1 100000 10
trajin Simu1_run2.mdcrd 1 100000 10
trajin Simu1_run3.mdcrd 1 100000 10
trajin Simu1_run4.mdcrd 1 100000 10
trajin Simu1_run5.mdcrd 1 100000 10
trajin Simu1_run6.mdcrd 1 100000 10
trajin Simu1_run7.mdcrd 1 100000 10
trajin Simu1_run8.mdcrd 1 100000 10
strip :WAT
strip :Na+
diffusion :1-53,55-67 1.0 average MSDs1tr_without54_WA


In this case there are 8 coordinate files of 5ns each that amount to a 40ns MSD simulation. The MSD plot averaged over 4 simulations is presented below.


Thanks for the help.

Best Regards,


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Received on Mon Jan 25 2021 - 01:00:02 PST
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