AMBER Archive (2009)

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

From: Jio M (jiomm_at_yahoo.com)
Date: Mon Nov 16 2009 - 23:13:44 CST

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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