RE: [AMBER] assigning velocities to each atom without heating the system

From: Ross Walker <>
Date: Mon, 2 Mar 2009 12:23:22 -0800

Hi Parimal,

> I am a novice to amber. I have created inpcrd and prmtop files loading
> the native structure into xleap. Now I want to perform MD. But I don't
> want to heat the system. How can I assign velocities to each atom without
> heating the system? Can we really do it in AMBER?

To follow up on what Gustavo said. If you mean by 'I don't want to heat the system' you mean you want it to REMAIN at 0 K then what Gustavo said applies. I.e. by having kinetic energy you by definition have a temperature. However, if you mean you would like to skip the 'heating' step and instead say just start your system at room temperature. What would be called a 'hot start' then you just need to set tempi=300.0. In this situation if irest=0, i.e. there are no velocities read from a restart file, then sander will generate a Boltzmann distribution of velocities that give 300.0K's worth of kinetic energy and assign these to the atoms.

Alternatively if you want to 'manually' assign velocities to each atom then you would need to modify the inpcrd file to include velocity entries and manually edit each value to give the velocity you want. This is of course tedious but I doubt this is what you meant.

Good luck,

|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
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Received on Wed Mar 04 2009 - 01:12:05 PST
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