AMBER Archive (2009)

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

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Tue Nov 17 2009 - 05:11:23 CST

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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