Re: [AMBER] Units in dist_vs_t file from SMD simulation

From: Xing <>
Date: Tue, 15 Aug 2017 00:08:24 -0400

Dear Dr. Roitberg,

I'm just starting using SMD. Now I understand that the first column is
distance (in Angstrom?), but what is the second column? I cannot find it
in the manual....

Thanks and best wishes,

On 05/07/2016 07:33 PM, Adrian Roitberg wrote:
> Hi Collin
> Indeed, the third column is force (vs t). The units are neither kcal/mol
> nor piconewtons.
> kcal/mol is a unit of energy not force.
> The correct units are (kcal/mol)/Angstrom
> On 5/6/16 5:08 PM, Nisler, Collin R. wrote:
>> Hello, I ran a steered molecular dynamics simulation using jar=1, and now have the dist_vs_t file. I am fairly certain that the third column of this file is the force of pulling at each step, but I am uncertain what its units are. Is this in kcal/mol, or in piconewtons? Thanks very much.
>> Collin Nisler
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Received on Mon Aug 14 2017 - 21:30:03 PDT
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