Previous Thread
Next Thread
Print Thread
question about error message!
#7905 08/17/05 07:36 AM
Joined: Jan 2005
Posts: 10
L
lwwd Offline OP
Forum Member
OP Offline
Forum Member
L
Joined: Jan 2005
Posts: 10
Hi!
all charmmers!
when i run my charmm script, such error is met!

CHARMM> skip all exclude elec
SKIPE> The following energy terms will be computed :
ELEC

CHARMM> nbonds inbfrq -1 atom cdiel switch cutnb 120 ctonnb 100 ctofnb 110

***** LEVEL -4 WARNING FROM *****
***** BAD BASE PASSED TO USEDDT
******************************************

i don't understand the meaning of this message and what fault leads to this error. What can i do to avoid this fault?

Thanks to all help!
best wish!

Re: question about error message!
lwwd #7906 08/17/05 08:12 AM
Joined: Sep 2003
Posts: 4,797
Likes: 2
Forum Member
Online Content
Forum Member
Joined: Sep 2003
Posts: 4,797
Likes: 2
Is this problem related to a particular script in the Script Archive?

You give no information about the charmm verrsion, os/hardware, molecular system, which in general helps when trying to resolve a problem.
This error may be related to problems in accessing more memory. Search the forums for "BAD BASE PASSED TO USEDDT" and see if anything seems to match your problem. A no-nonbond cutoff calculation on a large system could require substantial amounts of memory.


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden
Re: question about error message!
lennart #7907 08/17/05 09:05 AM
Joined: Jan 2005
Posts: 10
L
lwwd Offline OP
Forum Member
OP Offline
Forum Member
L
Joined: Jan 2005
Posts: 10
hi Lennart
Thanks for your reply!
the Charmm version is 29.1 and it is running on Dell computer with 2G memory, OS is Linux

In fact, the system we make research on is a complex(protien and protein ), about 350 residues included in this system. The interaction between two chains which include 100 residues is computed.

When the nonbond interaction is considered, the warning of this error is reported.

I have tried the command, such as " set stacksize unlimited " but the error message is still met.

I guess any relationship existing between the method we use, the parameter about nonbonds interaction, the switch function etc and the error.

By the way, i set the bomb -5. the computation can be finished with these error existing. Are these results we get in this processs credible?

Thanks! Best wish

Re: question about error message!
lwwd #7908 08/17/05 09:13 AM
Joined: Sep 2003
Posts: 4,797
Likes: 2
Forum Member
Online Content
Forum Member
Joined: Sep 2003
Posts: 4,797
Likes: 2
Results obtained with bomblev -5 cannot be trusted. bomblev -2 and lower should only be used when you fully understand what is going on.

You may want to try installing a larger (eg, install.com gnu large) version of CHARMM and/or reducing your cutoffs


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden
Re: question about error message!
lennart #7909 08/17/05 09:17 AM
Joined: Jan 2005
Posts: 10
L
lwwd Offline OP
Forum Member
OP Offline
Forum Member
L
Joined: Jan 2005
Posts: 10
Ok thanks!
I will try with reduced cutoff value

Re: question about error message!
lwwd #7910 08/17/05 05:57 PM
Joined: Sep 2003
Posts: 8,506
rmv Online Content
Forum Member
Online Content
Forum Member
Joined: Sep 2003
Posts: 8,506
There is a lengthy discussion of this particular error in the "Installation and Performance" forum; it's a bug triggered by HEAP expansion. There may be an unofficial patch available soon.

You can probably avoid the error by not using such large non-bond cutoffs, as it's that which triggers the HEAP expansion.


Rick Venable
computational chemist

Re: question about error message!
rmv #7911 08/18/05 04:19 AM
Joined: Jan 2005
Posts: 10
L
lwwd Offline OP
Forum Member
OP Offline
Forum Member
L
Joined: Jan 2005
Posts: 10
I am considering the electrostatistic interaction of nonbonds between two proteins. I are confused by the idea that when a reduced cut off value is set, an unpredictable affection will be led into the computational result, just because the attenuation radius of electrostatistic interaction differs from that of vdw interaction. Such error doesn't appear when the vdw nonbond interaction of same system is computed (the cutoff value of vdw is 999)

ps. In the charmm document,

ATOM CDIElec SHIFted
ATOM CDIElec SWITched

these two kinds of options are not recommonded,
but almost all scripts about the electrostatic interaction select these two options,i really want to know more about this field.

Really really thanks for all of your help!
Best wish

Re: question about error message!
lwwd #7912 08/18/05 04:30 PM
Joined: Sep 2003
Posts: 8,506
rmv Online Content
Forum Member
Online Content
Forum Member
Joined: Sep 2003
Posts: 8,506
Please post to the appropriate forum; the Script Archive is for sharing CHARMM scripts, and questions related directly to those scripts.

Re: question about error message!
lwwd #7913 08/18/05 07:05 PM
Joined: Sep 2003
Posts: 4,797
Likes: 2
Forum Member
Online Content
Forum Member
Joined: Sep 2003
Posts: 4,797
Likes: 2
Start by reading the paper cited in the CHARMM document just above the paragraph you quote.


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden

Moderated by  BRBrooks, lennart, rmv 

Link Copied to Clipboard
Powered by UBB.threads™ PHP Forum Software 7.7.4
(Release build 20200307)
Responsive Width:

PHP: 5.6.33-0+deb8u1 Page Time: 0.019s Queries: 32 (0.009s) Memory: 0.9620 MB (Peak: 1.0845 MB) Data Comp: Off Server Time: 2020-10-29 07:06:30 UTC
Valid HTML 5 and Valid CSS