AMBER Archive (2006)

Subject: Re: AMBER: dynamic memory allocation problem in nmode

From: Cenk Andac (
Date: Sun Mar 19 2006 - 03:10:22 CST

Hi again,
 I have installed Linux Suse x86_64 on my PC 64bit machine. I then
 nmode in 64 bit mode. I still get a similar error message that I
posted on 2.26.2006 as seen below.
 I have 1GB of dynamic memory and 5 GB of swap space. Would it be
possible to allocate the swap space to solve the memory problem with nmode ?
or Do I really have to do some shopping to get more memory sticks?
Also, I am wondering about the new nmode module of AMBER v9. How does nmode9 handles memory allocation problems in single unit PC computers? Is there anyway that nmode9 can use some harddisk space to expand its memory capacity in Linux x86_64 systems?
 best regards,
> On Sun, Feb 26, 2006, Cenk Andac wrote:
> >
> > Total memory required : 423592059 real words
> > ASSERTion ' ier == 0 ' failed in nmode.f at line
> > 105.
> You may simply have too large a system for your computer, especially
> it
> is a 32-bit OS. The system needs 432 million words, each 8 bytes
> or
> well over 3 Gbytes of memory. You probably need to find a 64-bit
> machine
> with lots of memory.
> ...good luck...dac

Jiten <> wrote:
  Hi I have posted similar error recently. However, I believe there is no
immediate solution for it. This is becuase you system probably has more than
4000 atoms (It is clearly mentioned in amber manual). I solved my problem by
by cutting out many/some of the residues (mostly at loop area) far from the
ligand. Of couse one needs to add C/N-terminal atoms. YOu may require to
minimize the system bit longer.

I hope it may help you,

Best wishes,

----- Original Message -----
From: "Cenk Andac"
Sent: Sunday, February 26, 2006 6:26 PM
Subject: Re: AMBER: dynamic memory allocation problem in nmode

> In addition to my previous message, I have also tried
> ismem=1 in my nmode input. However, ismem=1 did not
> work either.
> ..waiting for a solution to this.
> regards,
> jenk.
> --- Cenk Andac wrote:
>> Dear amber community,
>> I have been running entropy analysis for MD
>> snapshots
>> of a 54 KDa system (receptor+ligand) by the mm_pbsa
>> module of amber8. After sander minimization of the
>> system, the nmode analysis of the first snapshot
>> fails
>> giving the following error message.
>> Total memory required : 423592059 real words
>> Total memory required : 23938104 integer words
>> Maximum nonbond pairs 23505795
>> ASSERTion ' ier == 0 ' failed in nmode.f at line
>> 105.
>> As far as I know this message pops-up when there is
>> something wrong with dynamic memory allocation in
>> nmode. Could anyone of you know know how to
>> troubleshoot this problem?
>> regards,
>> jenk.

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