Re: Re: BOUNCE namd-l@ks.uiuc.edu: Message too long (>40000 chars)

From: snoze pa (snoze.pa_at_gmail.com)
Date: Tue May 06 2008 - 10:20:47 CDT

GC and NAMD users

The drop appear in rmsd profile is only dude to "fixedAtom off". So Do
you think i should not use "fixedAtom off"

This is very confusing situation. Because in all proteins(different
molecules) I am using same minimization(different cell size),
equilibration and full MD run and I am getting same profile.

Any help or suggestions.

Thank you very much.

S

On Mon, May 5, 2008 at 4:49 PM, snoze pa <snoze.pa_at_gmail.com> wrote:
> Dear NAMD users,
>
> (sorry jim for previous mail. A pdf file was attached in previous mail.)
>
> I did a small simulation using namd. A rmsd plot is also attached in
> this mail. I am little bit confused from the figure. As shown in the
> figure that the first 50ps of minimization it is working fine.
>
>
> Now in equilibration, another 100ps is working fine with the lengevin
> piston off.
>
> After that i am using the "fixedatom off" and minimize for 100 ps. In
> this case there is a sharp fall in rmsd as can be seen from the
> figure after 150ps step(50ps of minimization+100ps of minimization
> with lengevin piston off). Again after that it goes smoothly with
> step wise heating and finally full MD run till 2ns.
>
> Why the rmsd drop sharply at 151ps when "fixedatom off" is used. Am i
> doing alright or there is some problem.
>
> I am using the equilibration step taken from
>
>
> http://www.ks.uiuc.edu/Research/namd/tutorial/NCSA2002/hands-on/09_equil.html
>
> the namd.jpg file can be accessed via
>
> http://img519.imageshack.us/img519/9688/namdtx1.jpg
>
> Thank you very much for your help.
>
> s
>
>

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