AMBER Archive (2004)

Subject: AMBER: Re: constant pH calculation in Amber8

From: John Mongan (jmongan_at_mccammon.ucsd.edu)
Date: Thu Jul 29 2004 - 16:40:36 CDT

On Thu, 2004-07-29 at 14:00, yonchen wrote:
> Dear John Mongan:
>
> For the constant pH calculation, I want to make sure should I add -cpin
> flag to sander in minimization and equilibration procedures? I guess YES
> for equilibration but NO for minimization.

You need a cpin any time you have icsntph != 0. Depending on what you're
trying to equilibrate, you probably want this on for equilibration. You
can use it for minimization, where it is mainly useful if you wish to
minimize with a protonation state other than the default (you can set
the initial protonation state with the cpin file). If you do this, be
sure to set ntcnstph to something very large so you won't get any MC
steps during minimization.

>
> If SHAKE is used and the temperature is 310.16K, is 0.002 a safe value
> for the time step DT?

Generally, yes. It has worked for me.

>
> By the way, could you please tell me the available way to check the
> result of minimization and equilibration? As a new Amber user, the only
> instruction I could find is the tutorial materials. For the GB model
> application, there is only one example in DNA tutorial. But it is not
> enough for my case. I have finished a trial run but I got very big RMSD
> values (over 12). Therefore I guess I should find safe ways to check
> each step before I go to the next one. Could you give me some
> directions? Thank you so much!

I'm not sure exactly what you're asking. Generally the best way to check
the runs is to read carefully through the output files, to make sure
you've actually done what you think you've done and to look for errors.
For minimization you just want to make sure you've done enough cycles
that the energy is changing very slowly by the end. Equilibration is
much less important for GB than explicit solvent; in most of the
constant pH runs I've done, I skip equilibration as it doesn't seem to
make a difference. It is also often helpful to visualize the
trajectories or final molecule positions to make sure everything looks
OK. I assume the RMSD you mention was measured between starting and
ending structures? It sounds like either your system is coming apart or
perhaps you didn't fit the final structure to the initial before
measuring the RMSD -- you can get quite a lot of rotational and
translational motion in a GB trajectory. In either case, visualization
will help you determine what's going on.

John

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