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.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
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|\oss Walker
| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
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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
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Received on Wed Mar 02 2005 - 15:53:00 PST
