[gmx-users] gmx-users Digest, memory allocation error

[Justin A. Lemkul]

hema dhevi wrote:
> Dear all,
> 
> I am doing MD simulation for a bacterial inner transmembrane protein.
> I need to know which unit of lipid molecule i should take for building
> the lipid bilayer.
> 
> I made a trial run with DPPC. I was referring KAPL tutorial for my
> simulation. I made all the alteration in the topology file and in the 
> itp file, as it is mentioned in the
> tutorial but i wouldnt run after inflategro step ie during grompp i am
> getting memory allocation error.
> 
> Hereby I am attaching the erro r msg i got from grompp
> 
> 
> grompp -f ion.mdp -c system.pdb -p topol_protein.top -o ions.tpr
> 
> 
> Program grompp, VERSION 3.3.3
> Source code file: smalloc.c, line: 137
> 
> Fatal error:
> realloc for nnb->a[i][nre] (103103576 bytes, file topexcl.c, line 101, 
> nnb->a[i][nre]=0x0x33b3c3a0)
> ----------------------
> 
> "Can't You Make This Thing Go Faster ?" (Black Crowes)
> 
> : Cannot allocate memory
> Program grompp, VERSION 4.0.5
> Source code file: smalloc.c , line: 179
> 
> Fatal error:
> Not enough memory.
> Failed to realloc 244312864 bytes for nnb->a[i][nre], 
> nnb->a[i][nre]=0x22deb4d8 (called from file topexcl.c, line 102)
> -----------------------------
> --------------------------
> 
> "It's Against the Rules" (Pulp Fiction)
> : Cannot allocate memory
> 
> 
> I think i didnt made any error in file preparation and alteration of
> .itp and .top file. Because I tried it with 2 DPPC molecule it was
> working fine. when i am trying with the whole set of 128 molecules of
> DPPC i am facing this problem. Is this a problem something related to
> Memory of system if so what is the requirement for making this run
> possible.
> 

How many atoms are in your system?  How much memory do you have available on the 
machine you're using?  The general solutions can be found here:

http://www.gromacs.org/Documentation/Errors#Cannot_allocate_memory

-Justin

> I got struck up in my work I am highly in need of ur help...
> 
> 
> Thanks in advance< /span>
> 
> with regards,
> N.Hema Dhevi
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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