VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Thu Feb 21 2008 - 15:28:16 CST

On Thu, 21 Feb 2008, jrui_at_ci.uc.pt wrote:

RR> Hi,
RR>
RR> When I type the following commands in vmd console:
RR> mol new ADP01.mol2
RR> ls
RR> mol new ADP02.mol2
RR> ls
RR> ... and so on, everything goes fine. However, if try to read the different
RR> conformations as a trajectory:
RR> mol new ADP01.mol2
RR> ls
RR> mol addfile ADP02.mol2
RR> ls
RR>

RR> then I get the error "couldn't fork child process: not enough
RR> memory", although I still can load more frames to the molecule. The
RR> molecule has only 40 atoms (ADP). Other than that, vmd seems to work
RR> normally, except for calling linux commands and external programs
RR> (such as msms or tachyon). What could that be?

how long has your machine been running? how large are the files?
what else is running on that machine? how much swap do you have
configured?

it could quite likely be that you are simply running out of (virtual)
memory and that VMD has nothing to do with it. modern GUIs tend to have
a lot of gimmicks with sometimes serious memory leaks. also large
applications like webbrowsers, word processors, graphics tools etc.
tend to consume large quantities of address space and leak memory
like a sieve.

cheers,
   axel.

ps.: please check the status of your machine with running 'dmesg'
in a terminal and check if there is anything odd happening or run
'top' and then press Shift-M to see the top memory eaters.

RR>
RR> I'm using VMD 1.8.6 and Ubuntu 7.04, with 512MB RAM.
RR>
RR>
RR> Thanks,
RR> Rui Rodrigues
RR> 

-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.