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

hema dhevi hema_gromacs at
Mon Nov 30 07:15:13 CET 2009

 hi justin,thanks for your replyTotally I have 6126 atoms (residues + DPPC ) I am using the same pdb file and lipid pdb (DPPC128) which is given in the KAPL tutorial.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 aHP workstation with 2GB RAM.looking for ur reply at theearliest.Thanks in advancewith regards,N.Hema Dhevi Original message From:Justin A. Lemkul< jalemkul at >Date: 29 Nov 09 02:49:42Subject:Re: [gmxusers] gmxusers Digest, memory allocation errorTo: 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 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 t
 he 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 themachine you're using?The general solutions can be found here:> 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] | (540) 2319080 
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