AMBER Archive (2009)

Subject: Re: [AMBER] slope {no reply}

From: Sally Pias (sallypias_at_gmail.com)
Date: Wed Nov 18 2009 - 23:39:53 CST

It seems that you should be able to find data for the density of
dichloromethane at the appropriate temperature and pressure.
(Wikipedia lists a density value of 1.3266 g/cm³, which might be at
298 K and 1 atm -- http://en.wikipedia.org/wiki/Dichloromethane.)
This will give you an approximate figure for comparison with your
system. In my experience, protein systems solvated in water tend to
have a density slightly higher than 1 g/ml when equilibrated properly.
 This accounts for the greater density of a well-folded protein
compared to water alone. Perhaps you can extrapolate something
similar for your system, in order to help assess the quality of your
equilibration.

Sally Pias

On Tue, Nov 17, 2009 at 10:09 PM, Jio M <jiomm_at_yahoo.com> wrote:
> Thanks Carlos Simmerling and Bill Ross for replies and suggestions.
>
>
>
> Experimental data is lacking for my case :-( though I would try to search more for this.
>
>
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> thanks and regards;
>
> JIomm
>
>
>
>
>
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