AMBER Archive (2003)

Subject: Re: AMBER: MeCNBOX

From: Pascal Bonnet (pascal.bonnet_at_man.ac.uk)
Date: Fri Sep 26 2003 - 03:38:03 CDT

Dear Brain,

Take a look at these publications:
Acetonitrile, All atom:
Grabuleda X, Jaime C, Kollman PA
J. Comp. Chem. 2000,21,901
Molecular dynamics simulation studies of liquid acetonitrile: New six-site model

Acetonitrile, United atom:
Blas JR, Marquez M, Sessler JL, Luque FJ, Orozco M J. Am. Chem. Soc. 2002,124,12796
Theoretical study of anion binding to calix[4]pyrrole: the effects of solvent, fluorine substitution, cosolute, and water traces

Also, you can obtain this MeCN box (prep, box, frcmod) at the AMBER database updated by Richard Bryce (University of Manchester).
http://pharmacy.man.ac.uk/amber/

Pascal

*********** REPLY SEPARATOR ***********

On 25/09/2003 at 19:35 northrop_at_chem.ucla.edu wrote:

>Amber users - I'd like to run some simulations in an acetonitrile solvent
>but I don't know how to
>make a pre-equilibrated solvent box similar to those that exist for CHCl3,
>water, etc. The
>parameters I'm using for acetonitrile are those from the six-site model of
>Jaime et. al. (JOC,
> 21, 10, 901- 908). My procedure for trying to equilibrate a box of
>acetonitriile is as follows:
>in leap, I set the restype of MeCN to solvent and then solvate a 10 Å box
>on MeCN
>1000 step steepest descent minimization
>20 ps constant volume run to raise the temp to 300 k
>200 ps constant pressure run to equilibrate
>Unfortunately the program always fails with the error message "EWALD BOMB
>in subroutine,
>ewald_list, volume of ucell too big, too many subcells, list grid memory
>needs to be reallocated,
>restart sander." When I look at the restart file, there are large voids
>of no solvent within the
>periodic boundary. Any help anyone could give me about how to make a
>pre-equilibrated
>MeCNBOX would be greatly appreciated.
>
>thanks in advance,
>Brian Northrop
>
>-----------------------------------------------------------------------
>The AMBER Mail Reflector
>To post, send mail to amber_at_scripps.edu
>To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu