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

From: Adrian Roitberg <>
Date: Tue, 15 Aug 2017 09:22:52 -0600

Hi XIng

The amber16 manual says:

"The output file differs substantially from that used in the case of nmr
restraints. It contains 4 columns: x0(t), x,
force, work. Here work is computed as the integrated force over
distances (or angle, or torsion)."

So, the first column is the value of the coordinate you WANT the system
to have a particular time, interpolated between the initial and final
values by nstep/nstlim

The second column is the ACTUAL value of the coordinate at that same time.


On 8/14/17 10:08 PM, Xing wrote:
> 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,
> Xing
> 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
>>> _______________________________________________
>>> AMBER mailing list
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Dr. Adrian E. Roitberg
University of Florida Research Foundation Professor
Department of Chemistry
University of Florida
AMBER mailing list
Received on Tue Aug 15 2017 - 08:30:05 PDT
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