Re: How can I specify an exact initial velocity?

From: Jerome Henin (jhenin_at_cmm.chem.upenn.edu)
Date: Wed Nov 05 2008 - 03:56:46 CST

I see - then what you want is probably not a set initial velocity, but
a constant velocity enforced by steered MD? The KS website has a fair
amount of documentation on that:

http://www.ks.uiuc.edu/Research/smd_imd/
http://www.ks.uiuc.edu/Training/Tutorials/ (in the NAMD tutorial)

Best,
Jerome

On Tue, Nov 4, 2008 at 9:01 PM, wayj86 wayj86 <wayj86_at_gmail.com> wrote:
> Hi Jerome,
>
> I am trying to simulate the binding process. I want to specify an initial
> velocity (not a force) to the ligand and drive to it move towards the
> receptor. Do you think it is
> rational?
>
>
> Best wishes,
> Stanley
>
>
>
> 2008/11/4 Jerome Henin <jhenin_at_cmm.chem.upenn.edu>
>>
>> Hi,
>> So, you run crash tests for proteins, is that it?
>>
>> Seriously though, I think most people cannot see why one would want to
>> do this. Maybe you need to tell us a little bit more about what you
>> are trying to simulate (the big picture) - that will help people give
>> you the right advice.
>>
>> Best,
>> Jerome
>>
>> On Tue, Nov 4, 2008 at 3:29 AM, wayj86 wayj86 <wayj86_at_gmail.com> wrote:
>> > Hi everyone,
>> >
>> > I am trying to specify an exact initial velocity along x axis (100A/ns)
>> > to
>> > the whole protein (150 residues) to make it move along the x axis after
>> > it
>> > was equilibrated in periodic boundary condition. So what shall I do?
>> > Thank
>> > you very much for any help.
>> >
>> > --
>> > The future is now!
>> >
>
>
>
> --
> The future is now!
>

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