Dear Sir/Madam;
Thanks for taking interest. I have checked it also and quick web search
shows density to be 1.32 g/cc (25 degree C) and my simulation is at
300K (27 degree C) which gives density fluctuating at 1.2380 g/cc ( for
solvent dcm and macromolecule).... but if we see case of proteins (as
you have also replied) it should be somewhat higher.
Also If I see my output file
NSTEP = 100000 TIME(PS)
= 250.000 TEMP(K) =
299.31 PRESS = 59.6
Etot = 6178.0066
EKtot = 3863.0849
EPtot =
2314.9217
BOND =
674.1848 ANGLE =
1878.4011 DIHED
= 425.5195
1-4 NB = 189.5570 1-4
EEL = 4010.5437
VDWAALS = -4097.2245
EELEC = -766.0599
EHBOND =
0.0000 RESTRAINT
= 0.0000
EKCMT = 685.0976
VIRIAL = 563.0999
VOLUME = 94823.4042
Density
= 1.2380
PRESS is never 1. Is PRESS presented here in atm or other units.
its not only in my output but also in tutorial its never 1
(
http://ambermd.org/tutorials/basic/tutorial1/files/output_files/polyAT_wat_md2.out)
Should I conclude that
1) my dynamics conditions are not simulating natural environment which gives density of 1.3266 of solvent only
or
2) should I say my macromolecule is making empty pockets within itself
(I can see them) which makes system less dense as compared to the
otherwise condition of whole system was made of dcm solvent only of
same volume.
thanks and regards;
JIomm
--- On Thu, 11/19/09, Sally Pias <sallypias.gmail.com> wrote:
From: Sally Pias <sallypias.gmail.com>
Subject: Re: [AMBER] slope {no reply}
To: "AMBER Mailing List" <amber.ambermd.org>
Date: Thursday, November 19, 2009, 5:39 AM
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.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.
>
>
>
>
>
> thanks and regards;
>
> JIomm
>
>
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Thu Nov 19 2009 - 09:30:03 PST
