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

[Justin A. Lemkul]

hema dhevi wrote:
> 
> hi justin,
> 
> thanks for your reply
> 
> Totally I have 6126 atoms (residues + DPPC ) I am using the same pdb file
> and lipid pdb (DPPC-128) which is given in the KAPL tutorial.
> 

OK, just to clarify - are you working on the actual KALP tutorial when this 
error comes up, or are you working on your own system?  I am not 100% clear from 
what you've described.  Your previous message said you had some bacterial 
protein, and now you're talking about the KALP system.

Can you post the .mdp file you're using?

-Justin

> E ven tried it without adding any solvents to it, I am getting the same 
> error (memory allocation).
> 
> My system has 15.6 GB free space its a HP workstation with 2GB RAM.
> 
> looking for ur reply at the earliest.
> 
> Thanks in advance
> 
> with regards,
> N.Hema Dhevi
> 
> 
>     ---------- Original message ----------
>     From:Justin A. Lemkul< jalemkul at vt.edu >
>     Date: 29 Nov 09 02:49:42
>     Subject: Re: [gmx-users] gmx-users Digest, memory allocation error
>     To: hema dhevi , Discussion list for GROMACS users
> 
> 
> 
>     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
>      >
> 
>     -- 
>     ========================================
> 
>     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
> 
>     ========================================
> 

-- 
========================================

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

========================================