Re: NAMD feature request Hydrogenscale

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Wed May 30 2012 - 04:20:03 CDT

On Wed, May 30, 2012 at 3:36 AM, Norman Geist
<norman.geist_at_uni-greifswald.de> wrote:
> Hi Guys,
>
>
>
> I would like to do this feature request about a possibility to scale up the
> mass of hydrogen atoms within a simulation to be able to use larger
> timesteps with NAMD. As I think, many people need large simulation times for
> their systems like protein folding etc. The easiest way to increase this
> simulation time without much loss in computing time, precision and money, is
> to increase the timestep, if one is not looking for to fine grained
> mechanisms. Other simulation software like ACEMD provide such a parameter
> and make it possible to use a stable timestep of 4 fs while is scales up the
> hydrogens to the 4x mass and reducing the mass of the mother atom by the
> same amount, so that the total mass is constant.
>
>
>
> If I try to use such a large timestep with NAMD, I cannot get around this
> rattle constraint errors.

without commenting on scientific value, such a feature does
not require any changes to NAMD. just write a small (VMD)
script that transforms a psf file in a suitable way. you have
all the information you need and the psf file stores the masses.

axel.

>
>
>
> I would like you to share your opinions with me.
>
>
>
> Best wishes
>
>
>
> Norman Geist

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com http://goo.gl/1wk0
College of Science and Technology
Temple University, Philadelphia PA, USA.

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