AMBER Archive (2003)

Subject: Re: MD went crazy

From: Youyi Peng (pengyo_at_UMDNJ.EDU)
Date: Fri Apr 18 2003 - 14:28:14 CDT

Dear Dr. Simmerling:
   Thank you very much for you kindly help.
    I think I may use the inappropriate ref. structure for the restraint. The
ref. structure used is the inpcrd file saved from xleap, but not the restrt
strucrure from the previous MD run. After I used restrt structure from the
previous MD run, the restraint energy at step 1 is zero and the temp. doesn't
increase. I hope I am right this time.
   Thank a lot and have a nice weekend!
 Youyi

Carlos Simmerling wrote:

> at step 1 your restraint energy is still 10,000 kcal/mol.
> you need to figure out why your restraints do not
> match your input coordinates. at step 1, you should
> have nearly zero restraint energy (listed incorrectly by
> amber as CONstraint). When that happens, then you can
> do a production MD run and see what happens.
> Carlos
> ===================================================================
> Carlos L. Simmerling, Ph.D.
> Assistant Professor Phone: (631) 632-1336
> Center for Structural Biology Fax: (631) 632-1555
> Stony Brook University Web: http://comp.chem.sunysb.edu/carlos
> Stony Brook, NY 11794-5115 E-mail: carlos.simmerling_at_stonybrook.edu
> ===================================================================
>
> ----- Original Message -----
> From: "Youyi Peng" <pengyo_at_umdnj.edu>
> To: "Carlos Simmerling" <carlos.simmerling_at_stonybrook.edu>;
> <amber_at_heimdal.compchem.ucsf.edu>
> Sent: Friday, April 18, 2003 2:55 PM
> Subject: Re: MD went crazy
>