Re: [AMBER] Problems with TIP5P water

From: Ross Walker <>
Date: Tue, 25 Jan 2011 08:31:53 -0800

Hi Tommaso,

> I am trying to simulate a solution of propylene glycol and water,
> using TIP5P model. I put 6000 water molecules and 637 pg molecules in
> a box of 60 A.

How did you set up this solution? Specifically did you start with an
equilibrated box of propylene glycol and then add water to it using
solvatebox in Leap or did you somehow create a mixture of the two? Chances
are you have molecules on top of each other in your initial structure and
this is what is causing the problem.
> When I run the minimization step, EEL value rises too much and
> minimization fail.

You should also check your parameters for propylene glycol. Are the charges
correct, is the system neutral?

> Minimization step is carried out with a cut off of 15 A.

I assume you are running periodic boundaries with PME? - In which case you
should set the cut off to 8 A. You should check you have ntb=1,ntp=1 as well
so you do the minimization with constant volume.

All the best

|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Adjunct Assistant Professor |
| Dept. of Chemistry and Biochemistry |
| University of California San Diego |
| NVIDIA Fellow |
| | |
| Tel: +1 858 822 0854 | EMail:- |

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Received on Tue Jan 25 2011 - 09:00:04 PST
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