AMBER Archive (2009)

Subject: Re: [AMBER] MM-GBSA nmode error for explicit solvent system only but not for implicit solvent system. Why?

From: Ashish Runthala (ashish.runthala_at_gmail.com)
Date: Sat Aug 15 2009 - 22:59:11 CDT

Ya there are there catherine. Tell me which OS you are working on?
Also tell me the size of your RAM and the available free hard disk
space in the partition where you have installed your OS.

2009/8/16 Catein Catherine <askamber23_at_hotmail.com>:
>
> Thank you Ashish,
>
>
>
> I did the analysis with single CPU computer. If I cannot add physical memory to the system, are there any other way to solve this problem?
>
>
>
> Best regards,
>
>
>
> Cat
>
>> Date: Sat, 15 Aug 2009 11:35:53 +0530
>> Subject: Re: [AMBER] MM-GBSA nmode error for explicit solvent system only but not for implicit solvent system. Why?
>> From: ashish.runthala_at_gmail.com
>> To: amber_at_ambermd.org
>>
>> Total memory required : 1604498119 real words
>> > Total memory required : 60129519 real words
>> > ASSERTion 'ier ==0' failed in nmode.f at line 105.
>>
>> Amber's nmode is not a parallel program, so it cannot make use of any memory
>> except that available to the cpu that is running the code.
>> You have not mentioned the number of nodes you are accessing for it. But
>> they are definitely not sufficient for your calculation.
>>
>> Don't worry. This is a common problem to a parallel systems.
>> Although nodes are allocated to share CPUs, random access memories are
>> somewhat not shared or not allowed to share high amount of memory. I advise
>> you to ask the computer facility guide there, to allocate physical memories
>> among different nodes.
>> So
>>
>> Ashish Runthala,
>> Faculty Division III,
>> Assistant Lecturer, Biological Sciences,
>> Birla Institute of Technology and Science,
>> Pilani, Rajasthan- 333031
>> INDIA
>> _______________________________________________
>> AMBER mailing list
>> AMBER_at_ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
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-- 
Ashish Runthala,
Faculty Division III,
Assistant Lecturer, Biological Sciences,
Birla Institute of Technology and Science,
Pilani, Rajasthan- 333031
INDIA

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