Re: [AMBER] How to assign initial velocities (directly not by increasing temeperature) to water molecules

From: Adrian Roitberg <>
Date: Tue, 30 Jul 2013 17:45:21 -0400

Dear Yan

The easiest thing to do is run a regular MD with amber velocities, for a
short time, and look at thew restart file after the run is finished.
That will give you a template to change the velocities.

After you are done, you need to do ntx=5 and also irest=1, which tells
amber to use velocities from the restart file.


On 7/30/13 5:42 PM, Yan Duan wrote:
> Dear Amber developers and users:
> Hi, I'm a new user of this powerful molecular dynamics software. As I've
> asked this problem in the group weeks ago, still I have some questions
> regarding the very same issue.
> As I've searched around for days, seems that very few people did this
> before: although I know that Amber assign a distribution of velocities
> according to the temperature, but what if I'd like to assign specific
> velocities directly to the atoms, not by increasing the temperature?
> Many thanks to Jason Swails,
> I understood that I could do this by modifying the .inpcrd file. But
> could you please explain this in some more details? For example, now I did
> try to add thousands of lines below the coordinates of atoms in the .inpcrd
> file, but how could I let Amber process the modified file? I mean should I
> simply add a line of "ntx=5" in the &cntrl and that's it? Or does .inpcrd
> file requires a specific format to let Amber read its velocites
> information? Since till now my modified .inpcrd file could still not be
> accepted by Amber.
> So many thanks for reading this long question and I'm looking forward for
> your response!
> Many thanks,
> Yan
> _______________________________________________
> AMBER mailing list

                             Dr. Adrian E. Roitberg
Colonel Allan R. and Margaret G. Crow Term Professor.
Quantum Theory Project, Department of Chemistry
University of Florida
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Received on Tue Jul 30 2013 - 15:00:03 PDT
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