Re: [AMBER] minimization difficulties

From: David A Case <>
Date: Mon, 3 Dec 2018 10:05:32 -0500

On Mon, Dec 03, 2018, Kimia Sh wrote:

>I have just accomplished a minimization process and i have attained three
>minout data (minout 1,2 and 3) in which minout1 data has abnormal energy
>level for first step(which is +9.19e+16) however remaining steps have
>normal values starting with -1.91e+05 (for second step) and decreasing
>small amount step by step, as well as both minout 2 and 3 have normal
>values for first step.
>can i proceed for MD with such error ignoring first step and considering
>remaining step?

Depending on how you set up the system, it is not unusual to have a bad
clash of atoms that leads to a high energy at the first step. This can
usually be ignored if minimization removes such bad contacts, but you
should certainly want to examine the minout1 structure to see if it
looks like any problems are present.


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Received on Mon Dec 03 2018 - 07:30:02 PST
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