AMBER Archive (2007)

Subject: Re: AMBER: Is the simulation reasonable ? (SMD : dissocation antibody-antigen)

From: Adrian Roitberg (roitberg_at_qtp.ufl.edu)
Date: Thu May 17 2007 - 10:06:49 CDT

wang wrote:
> Dear all ,
> My simulation is aimed to dissocate the antibody-antigen and
> used. My result is showed below :
>
> x0(t) x force work
> (kcal/mol)
> ...................................................................................
>
>
> 262.99600 262.95780 76.39850 2839.89123
> 262.99700 262.98146 31.07620 2839.94496
> 262.99800 263.00201 -8.01038 2839.95650
> 262.99900 263.00664 -15.28246 2839.94485
>
>
> I think the work is very large . And every body , Did you think
> it is reasonable ?
>
> thanks
> wang
>
>
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I guess this one is for me ;-)

First, make sure you apply the bugfixes to the code, there at least one
related to smd.

Second: indeed, the work is very large, but that can depend on many
factors. How fast did you pull ? are you pulling center of mass of
groups of atoms ? what was your force constant ? how much was the pull ?
Without those, it would be very hard to tell if this is reasonable.
So pleae, email me your mdin and mdout files to start with.

PS: email those just to me, NOT the list.
Thanks ! 

-- 
                            Dr. Adrian E. Roitberg
                              Associate Professor
               Quantum Theory Project and Department of Chemistry

University of Florida                         PHONE 352 392-6972
P.O. Box 118435                               FAX   352 392-8722
Gainesville, FL 32611-8435                    Email adrian_at_qtp.ufl.edu
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