AMBER Archive (2009)

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

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Tue Nov 17 2009 - 17:49:39 CST

the density of solvent only would be a good start. if you had questions
about your solvent model you could run a simulation of pure solvent and see
if it matches expt. you can also check the papers for this solvent model, if
it was published.

On Tue, Nov 17, 2009 at 2:13 PM, Jio M <jiomm_at_yahoo.com> wrote:

> 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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> >
> >
> >
> >
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