AMBER Archive (2009)

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

From: Jio M (jiomm_at_yahoo.com)
Date: Tue Nov 17 2009 - 13:13:06 CST

Dear Sir,

(Thanks to Bill Ross also for reply)

> actual (experimental) density of that "//liquid//"

I am still a learner may (or must) be wrong;  please correct and pardon me

"liquid" that is being mentioned here, does it mean only solvent (that
is dichloromethane that I have used) or solute in solvent.I mean to say
that if we see the output file for density and volume "or "also if we
use solvateoct (which also shows the 'mass' in amu along with density
and volume) density term considers the whole mass solute + solvent.

So I  think, I have to look experimental data for density of
solute in solvent at 300K and 1 atm i.e. Lab conditions but not for
density of dcm at 300K

thanks, regards and pardons;

JIomm

--- On Tue, 11/17/09, Carlos Simmerling <carlos.simmerling_at_gmail.com> wrote:

From: Carlos Simmerling <carlos.simmerling_at_gmail.com>
Subject: Re: [AMBER] slope {no reply}
To: "AMBER Mailing List" <amber_at_ambermd.org>
Date: Tuesday, November 17, 2009, 11:11 AM

what is the actual (experimental) density of that liquid under the same
temperature/pressure as you are simulating?

On Tue, Nov 17, 2009 at 12:13 AM, Jio M <jiomm_at_yahoo.com> wrote:

> Dear Sir ,
>
> (Bill Ross)
>
>
>
> >Try it and see - allow big clearance since density will be low
>
> >since the molecule will be placed in a grid rather than be packed
>
>
>
> I have done this and last step of equilibration gives this:
>
>
>
> 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
>
>  Ewald error estimate:   0.1530E-03
>
>
>
> what conclusion can we draw from output regarding density (low or high);
> please suggest .
>
> At equilibrium, the density vs time plot gives approx. constant
> density. Is it sufficiently suggesting that I can use single molecule
> as a solvent..
>
>
>
> thanks and regards;
>
> JIomm
>
>
>
>
>
> --- On Mon, 11/16/09, Bill Ross <ross_at_cgl.ucsf.edu> wrote:
>
> From: Bill Ross <ross_at_cgl.ucsf.edu>
> Subject: Re: [AMBER] slope {no reply}
> To: amber_at_ambermd.org
> Date: Monday, November 16, 2009, 5:48 PM
>
> > 2) same query as before.. can we solubilize the system with single
> molecule
> > instead of box solvent
>
> Try it and see - allow big clearance since density will be low
> since the molecule will be placed in a grid rather than be packed.
>
> Bill
>
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