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.cgl.ucsf.edu> wrote:
From: Bill Ross <ross.cgl.ucsf.edu>
Subject: Re: [AMBER] slope {no reply}
To: amber.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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Received on Mon Nov 16 2009 - 21:30:03 PST
