<br>hi justin,<br><br>thanks for your reply<br><br>Totally I have 6126 atoms (residues + DPPC ) I am using the same pdb file <br>and lipid pdb (DPPC-128) which is given in the KAPL tutorial.<br><br>E ven tried it without adding any solvents to it, I am getting the same error (memory allocation).<br><br>My system has 15.6 GB free space its a HP workstation with 2GB RAM.<br><br>looking for ur reply at the earliest.<br><br>Thanks in advance<br><br>with regards,<br>N.Hema Dhevi<br><blockquote><br>---------- Original message ----------<br>From:Justin A. Lemkul< jalemkul@vt.edu ><br>Date: 29 Nov 09 02:49:42<br>Subject: Re: [gmx-users] gmx-users Digest, memory allocation error<br>To: hema dhevi <hema_gromacs@in.com>, Discussion list for GROMACS users <gmx-users@gromacs.org><br><br><br>
<br>
hema dhevi wrote:<br>
> Dear all,<br>
> <br>
> I am doing MD simulation for a bacterial inner transmembrane protein.<br>
> I need to know which unit of lipid molecule i should take for building<br>
> the lipid bilayer.<br>
> <br>
> I made a trial run with DPPC. I was referring KAPL tutorial for my<br>
> simulation. I made all the alteration in the topology file and in the <br>
> itp file, as it is mentioned in the<br>
> tutorial but i wouldnt run after inflategro step ie during grompp i am<br>
> getting memory allocation error.<br>
> <br>
> Hereby I am attaching the erro r msg i got from grompp<br>
> <br>
> <br>
> grompp -f ion.mdp -c system.pdb -p topol_protein.top -o ions.tpr<br>
> <br>
> <br>
> Program grompp, VERSION 3.3.3<br>
> Source code file: smalloc.c, line: 137<br>
> <br>
> Fatal error:<br>
> realloc for nnb->a[i][nre] (103103576 bytes, file topexcl.c, line 101, <br>
> nnb->a[i][nre]=0x0x33b3c3a0)<br>
> ----------------------<br>
> <br>
> "Can't You Make This Thing Go Faster ?" (Black Crowes)<br>
> <br>
> : Cannot allocate memory<br>
> Program grompp, VERSION 4.0.5<br>
> Source code file: smalloc.c , line: 179<br>
> <br>
> Fatal error:<br>
> Not enough memory.<br>
> Failed to realloc 244312864 bytes for nnb->a[i][nre], <br>
> nnb->a[i][nre]=0x22deb4d8 (called from file topexcl.c, line 102)<br>
> -----------------------------<br>
> --------------------------<br>
> <br>
> "It's Against the Rules" (Pulp Fiction)<br>
> : Cannot allocate memory<br>
> <br>
> <br>
> I think i didnt made any error in file preparation and alteration of<br>
> .itp and .top file. Because I tried it with 2 DPPC molecule it was<br>
> working fine. when i am trying with the whole set of 128 molecules of<br>
> DPPC i am facing this problem. Is this a problem something related to<br>
> Memory of system if so what is the requirement for making this run<br>
> possible.<br>
> <br>
<br>
How many atoms are in your system? How much memory do you have available on the <br>
machine you're using? The general solutions can be found here:<br>
<br>
http://www.gromacs.org/Documentation/Errors#Cannot_allocate_memory<br>
<br>
-Justin<br>
<br>
> I got struck up in my work I am highly in need of ur help...<br>
> <br>
> <br>
> Thanks in advance< /span><br>
> <br>
> with regards,<br>
> N.Hema Dhevi<br>
> <br>
<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]vt.edu | (540) 231-9080<br>
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin<br>
<br>
========================================</gmx-users@gromacs.org></hema_gromacs@in.com></blockquote>