AMBER Archive (2009)

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

From: Catein Catherine (askamber23_at_hotmail.com)
Date: Mon Aug 17 2009 - 00:58:49 CDT

Dear Ross,

 

I see. Thank you very much for your help. Are there anything to do with how I prepare the snapshot? It seems to me that I should strip all the water from the mdcrd files before doing MM-GBSA analysis. If it is the case, how can I do it?

 

Best regards,

Cat

 
> From: ross_at_rosswalker.co.uk
> To: amber_at_ambermd.org
> Subject: RE: [AMBER] MM-GBSA nmode error for explicit solvent system only but not for implicit solvent system. Why?
> Date: Sat, 15 Aug 2009 21:40:26 -0700
>
> Hi Cat,
>
> Sometimes it helps just to take a careful look at the error message rather
> than going to all the trouble of specifying your system specs etc. In your
> case you will see that nmode is asking for:
>
> Total memory required : 1604498119 real words
>
> In Fortran 1 word = 8 bytes so in your case this is 12835984952 bytes. This
> is equivalent to 11.95GB. Thus you need at least 16GB available to you - so
> you are not swapping. Unless you have some high end workstation it is
> unlikely your machine can be upgraded for this much ram. You could check on
> using some large shared memory machines such as are available on the US
> teragrid system. E.g. Pople the SGI Altix at PSC. Of course this is still a
> very expensive simulation so you might want to see if you can cut down the
> size of your system or look for alternative approaches such as principle
> component analysis techniques. Maybe others on the list can comment more.
>
> Good luck,
> Ross
>
> > -----Original Message-----
> > From: amber-bounces_at_ambermd.org [mailto:amber-bounces_at_ambermd.org] On
> > Behalf Of Catein Catherine
> > Sent: Saturday, August 15, 2009 9:13 PM
> > To: amber_at_ambermd.org
> > Subject: RE: [AMBER] MM-GBSA nmode error for explicit solvent system
> > only but not for implicit solvent system. Why?
> >
> >
> > Thank you Ashish,
> >
> >
> >
> > I am using red hat linux, with 2-5G free hard disk in running directory
> > but less than 1 G in the partition where I installed the OS. I may
> > have ~1G RAM, but i am not sure. Please kindly instruct.
> >
> >
> >
> > Best regards,
> >
> > Cat
> >
> > > Date: Sun, 16 Aug 2009 12:59:11 +0900
> > > 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
> > >
> > > 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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> > > AMBER_at_ambermd.org
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> >
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