AMBER Archive (2007)

Subject: Re: AMBER: &dipole input and some questions on using polarizable force fields

From: Seongeun Yang (seongeun_at_korea.ac.kr)
Date: Tue Oct 30 2007 - 09:19:32 CST

> You need to equilibrate to 300 K before turning on constant pressure. That
> is, try doing a constant volume simulation first. Also, what is your initial
> density?
>
> You may need to use a larger box, i.e. a bigger value than 8.0 in the
> solvateoct command. Sander can run into the problems you see when trying to
> simulate very small (by our standards!) systems.
>

Thanks for your reply, but I should say the followings.
When I heat the system to temperature of interest, I use NPT condition.
Because the initial density generated in leap is much lower than the value at ambient temperature.
Then, I equilibrat the system at the temperature of interest uner NVT condition for a while
until the density reaches the appropriate value.
And then the production run is done with either NPT or NVT condition.
Is there any problem with this procedure?
I didn't see any problem till now, even with "solvateoct" with nonpolarizable force fields.

Thanks anyway.

Seongeun
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