Tutorial-l Mailing List
From: Sridhar Kumar Kannam (srisriphy_at_gmail.com)
Date: Thu Apr 04 2013 - 21:26:57 CDT
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Thanks Paul,
The problem is solved by using the Nightly Build (2013-04-04) Platforms
Best,
On Thu, Apr 4, 2013 at 10:59 AM, Paul Sebexen <paul_at_evosol.co> wrote:
> Dear Sir,
>
> It sounds as if the error is likely due to an improper build of NAMD. I
> have seen very similar errors resolved by compiling with a correct set of
> flags.
> For diagnostic purposes, it would be useful to know if you encounter the
> same problem on another computer when adding SiN to the system.
>
> I hope this is helpful.
>
> Best regards,
> Paul
>
>
> ___________________
> *Paul Sebexen*
> *Evolutionary Solutions Incorporated*
> CEO, Co-Founder
>
>
> On Wed, Apr 3, 2013 at 4:03 PM, Sridhar Kumar Kannam <srisriphy_at_gmail.com>wrote:
>
>> Dear NAMD users.
>>
>> I am working on tutorial - *Modeling Nanopores for Sequencing DNA.*
>>
>> I increase the pore length and diameter and my new system contain around
>> 3 million atoms. I am working on compressing the system using
>> genCompressedPsf to use NAMD memory reduction version. But I am getting the
>> error - FATAL ERROR: Memory allocation failed on processor 0.
>>
>> The compression is working fine when I have only protein and water as the
>> system.
>> I am having the problem when I have SiN (generated using inorganic
>> builder) or graphene (generated using nanotube builder) as a part of the
>> system.
>>
>>
>> I have 16GB memory on the node I am using. The error is not really due to
>> the memory problem on the node but when I have SiN as a part of the system.
>>
>> Can anyone please suggest me a way around ....
>>
>>
>>
>> Thank you very much.
>>
>>
>> --
>> Cheers !!!
>> Sridhar Kumar Kannam :)
>>
>>
>>
>>
>
-- Cheers !!! Sridhar Kumar Kannam :) ** ** Visit http://www.greatcircle.com/majordomo/ for more info on majordomo **
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