VMD-L Mailing List

From: jrui_at_ci.uc.pt
Date: Fri Feb 22 2008 - 08:41:54 CST

Sorry, I forget to "reply-all" to John Stone's request. Please find attached 3
mol2 files, for different conformations of the same molecule. They were
obtained with marvin (chemaxon).
Thanks,
Rui Rodrigues

Quoting Peter Freddolino <petefred_at_ks.uiuc.edu>:

> Hi Rui,
> it would be helpful if you could send the culprit mol2 file so we can
> check what was causing the problems.
> Thanks,
> Peter
>
> jrui_at_ci.uc.pt wrote:
>> Hi,
>>
>> The error arises even after a fresh OS restart. The files are small:
>> ~2KB each.
>> I can load all my mol2 files as separates molecules: the error arises when I
>> try to load the files as a trajectory (in a new vmd session), right
>> after the
>> second frame.
>> I have 512MB swap and 512MB RAM. When I start VMD, it tells me that there is
>> 375MB of free system memory (74%).
>> The main memory eaters are Xorg (5.5%) and vmd (5.0%).
>> I could not find anything strange in the dmesg output, but i'm not
>> sure what I
>> should be looking for... :)
>>
>> Here is the output of the "free" command before starting VMD:
>>
>> total used free shared buffers cached
>> Mem: 513932 376448 137484 0 10272 219236
>> -/+ buffers/cache: 146940 366992
>> Swap: 506008 0 506008
>>
>> Here is the output of "free" after launching VMD:
>> Mem: 513932 376508 137424 0 10328 219260
>> -/+ buffers/cache: 146920 367012
>> Swap: 506008 0 506008
>>
>> And here is the output of "free" after I load two files as a trajectory:
>> Mem: 513932 376656 137276 0 10436 219252
>> -/+ buffers/cache: 146968 366964
>> Swap: 506008 0 506008
>>
>>
>> For now, I converted my mol2 files to pdb files and load them as a
>> trajectory
>> and it works fine.
>>
>> Thanks,
>> Rui Rodrigues
>>
>>
>>
>>
>> Quoting Axel Kohlmeyer <akohlmey_at_cmm.chem.upenn.edu>:
>>
>>> 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.
>>>
>>>
>>
>>
>>
>
>