AMBER Archive (2008)

Subject: Re: AMBER: SPCFW problems

From: Naser Alijabbari (na3m_at_virginia.edu)
Date: Tue Oct 28 2008 - 10:50:49 CDT

Thanks Dr. Case,
Turning off 'fast SHAKE' stopped the error. I will try the MD part with
1fs timestep.
So I am guessing for SPCFW

- WAT = SPF

- set WAT.1 name 'SPF'

doesn't do anything because I don't see a change in my prmtop file.

But I think the SPCFW water is used since there is no complaint from these
commands.

- loadAmberParams frcmod.spcfw
- set default FlexibleWater on

On Tue, Oct 28, 2008 at 6:49 AM, David A. Case <case_at_biomaps.rutgers.edu>wrote:

> On Mon, Oct 27, 2008, Naser Alijabbari wrote:
>
> > I am having problems getting the SPCFW water working.
> > steps in tleap (I have added "?." To keep the file short):
> >
> >
> > Error: A residue defined as a "fast 3-point water"
> > is not defined by a triangle of three bonds.
>
> Try setting jfastw=4. Of course, this should not be necessary, since you
> didn't ask for SHAKE anyway. But the code calls a setup routine for SHAKE,
> even when SHAKE has not been invoked :-(
>
> And, check the calculations carefully. As you can tell, not many Amber
> calculations have actually been done with flexible waters. You may need
> quite
> a short time step to get good results.
>
> ...dac
>
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