AMBER Archive (2005)

Subject: Re: AMBER: about run time in GB and PB

From: Phineus Markwick (markwick_at_embl-heidelberg.de)
Date: Thu Apr 21 2005 - 09:10:20 CDT

Dear Yong Xu,

did you perform a short energy minimisation of the system before heating
and equilibrating at 300K?

Have you actually _looked_ at the simulation to see what is going on?
You might have just forgotten to
remove the translational/rotational motion before calculating the rmsd,
or, if you are referring to the rmsd of
the complex, then maybe the ligand is moving away from the protein, and
one might need some restraints to
hold this... but you are only going to know what's going on if you set
ntpr=1 and look at the simulation at each step
to see where you are having problems... ptraj will give you the rmsd,
but it won't tell you where your problems are.

By the way, have you looked at the tutorials available at the amber
website? They provide examples of
running MD simulations in explicit or implicit solvent, and also on how
to analyse the trajectory.
Maybe you could follow their example, using your protein, rather than
the protein-ligand complex to see if you can get
a stable trajectory for just the protein first....

with best regards,
Phin.

Yong Xu wrote:

>Dear Prof. Duan and Phineus
>
>thank you for all your reply.
>I re-evaluated the time need for MD.
>the information shown in my previous mail is the heating process . During that process, I use position constraint to mainchain. when I run production MD, I loose all atom. the speed of MD is about 1/5-1/4 comparing with GB method.
>
>another problem arising.
>when I release all atoms without restraint, the RMSD of whole protein reach to 4-6 angstrom within 60ps.
>that is to say, the whole system crash.
>
>should I restraint something again, like Ca or mainchain?
>is it correct to analysis result using traj with distance-restraint, angle-restraint, or position constraint for some atoms?
>
>Yong
>

>

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