AMBER Archive (2005)

Subject: RE: AMBER: NaNQ

From: ilaria massarelli (ilariama_at_yahoo.it)
Date: Wed Mar 02 2005 - 09:01:33 CST


Thank you very much for your suggestion,
I changed the restraint in the input of the MD and the results seem going better....

Ross Walker <ross_at_rosswalker.co.uk> wrote:
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_at_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_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of ilaria massarelli
Sent: 01 March 2005 00:45
To: amber_at_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

---------------------------------
Nuovo Yahoo! Messenger E' molto più divertente: Audibles, Avatar, Webcam, Giochi, Rubrica… Scaricalo ora!
                                
---------------------------------
Nuovo Yahoo! Messenger E' molto più divertente: Audibles, Avatar, Webcam, Giochi, Rubrica… Scaricalo ora!
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu