AMBER Archive (2006)

Subject: RE: AMBER: vlimit exceeded for step 0, vmax = infinity

From: Yong Duan (duan_at_ucdavis.edu)
Date: Fri Nov 10 2006 - 15:55:23 CST

Hi, Rachel,

I wonder what would happen if you set ntc=3 in minimization and MD. I know
it will not converge and I understand this is not recommended by the manual,
but just perform a 100-step minimization after you do those "standard"
minimization.

Another wild guess, could it be possible that one of the atoms in your
system has zero mass? If it is a very high velocity, it will say a number of
a lovely "****". But, if the print out is "Infinity", it means "divided by a
zero" somewhere. This could either be two atoms happen to be right on top of
each other or some atoms are simply massless.

Another suggestion is to try simulations on the individual components to
identify which part of the system may cause the trouble.

Good luck!

yong
-----Original Message-----
From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
Rachel
Sent: Friday, November 10, 2006 7:54 AM
To: amber_at_scripps.edu
Subject: Re: AMBER: vlimit exceeded for step 0, vmax = infinity

Hi, all,

I followed the tutorial 1 and the tutorial of non-standard residue, and i
did try to simulate only the hydrogen molecule with explicit water and it
was fine as well :(

Any other suggestions, now i really dont know where shall i start to solve
the problem ::>_<:: any suggestion will be greatly appreciated.
 
best regards,
Rachel
 

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