Re: [AMBER] how to restart a molecular dynamics simulation

From: Hector A. Baldoni <hbaldoni.unsl.edu.ar>
Date: Tue, 5 Mar 2013 17:22:49 -0300 (ARGSL-ST)

Hi! Emilio,

Next time you could run a long MD by fragments of 2ns using a customized
as the attached script.

just in case! (por si las moscas!)

Hector.


>
>
>
>
> Dear All
> I need to restart a molecular dynamics calculation that was stopped due to
> a power outage.
> What restart/coordinate file should I put in the command line when calling
> pmemd (i.e., in the -c flag), the input rst/inpcrd file used in the last
> simulation or the output restart file from the dynamics I want to restart?
> Similarly, what reference file should I put in the command line when
> calling pmemd (i.e., in the -ref flag), the rst/inpcrd file from the
> original simulation or the output restart file from the dynamics I want to
> restart?
> If the second choice is the correct one, another question is how to
> generate the output restart file from the trayectory since the current
> .rst written to disk is truncated.
> Thank you
> Emilio
>
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
>


--------------------------------------
 Dr. Hector A. Baldoni
 Area de Quimica General e Inorganica
 Universidad Nacional de San Luis
 Chacabuco 917 (D5700BWS)
 San Luis - Argentina
 hbaldoni at unsl dot edu dot ar
 Tel.:+54-(0)266-4423789 ext. 157
--------------------------------------

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Received on Tue Mar 05 2013 - 12:30:04 PST
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