Dear Ilaria,
NaN essentially means Not a Number or infinity. It is generally generated by
dividing by zero. The source of this problem is the *****'s. When sander
cannot fit a number in the output space provided it instead prints *****'s
typically you should never see this as the output spaces have been chosen to
match the sizes of numbers expected from a simulation. Thus the ****'s mean
something is seriously wrong. The problem in your case is with your
restraints. The restraint energy is huge which is leading to a massive
potential energy and therefore a massive temperature. I would check your
restraint definitions carefully before running more simulations.
All the best
Ross
/\
\/
|\oss Walker
| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- ross.rosswalker.co.uk |
| <
http://www.rosswalker.co.uk/>
http://www.rosswalker.co.uk/ | PGP Key
available on request |
Note: Electronic Mail is not secure, has no guarantee of delivery, may not
be read every day, and should not be used for urgent or sensitive issues.
_____
From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf Of
ilaria massarelli
Sent: 01 March 2005 00:45
To: amber.scripps.edu
Subject: AMBER: NaNQ
Good morning,
I had some problems with sander. In some runs of MD of a protein-ligand
complex I obtained the label -NaNQ and a lot of ******** for several terms
during the sander run. I report here an example. This is a fragment of a 15
ps equilibration at 300 K performed after an heating of 5 ps from 0 to 300K.
NSTEP = 14500 TIME(PS) = 19.500 TEMP(K) =********* PRESS = 0.0
Etot = -NaNQ EKtot = ************ EPtot = -NaNQ
BOND = 734.0641 ANGLE = 1856.5024 DIHED = 2728.0707
1-4 NB = 924.8968 1-4 EEL = 13059.3943 VDWAALS = -2205.6991
EELEC = -17879.4424 EGB = -NaNQ RESTRAINT = ************
ESURF = 51.0843
EAMBER (non-restraint) = -NaNQ
What do they mean? And how can I solve this problem?
thank you
Ilaria Massarelli
_____
<
http://it.rd.yahoo.com/mail/taglines/*http://it.messenger.yahoo.com> Nuovo
Yahoo! Messenger E' molto pił divertente: Audibles, Avatar, Webcam, Giochi,
Rubrica… Scaricalo ora!
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Tue Mar 01 2005 - 16:53:00 PST
