[gmx-users] gmx-users Digest, Vol 67, Issue 142

hema dhevi hema_gromacs at in.com
Sat Nov 28 10:27:22 CET 2009

 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 buildingthe lipid bilayer. I made a trial run with DPPC. I was referring KAPL tutorial for mysimulation. 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 during grompp iam getting memory allocation error. I tried it with two versions of gromacs 3.3.3 and 4.0.5 versions I am getting the same error. and I tried it running in hp workstation and also in server.inflategro output pdb= system.pdbHereby I am attaching the error msg i got from gromppgromppf ion.mdp c system.pdb p topolprotein.top o ions.tprProgram grompp, VERSION 3.3.3Source code file: smalloc.c, line: 137Fatal 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 mem
 oryProgram grompp, VERSION 4.0.5Source code file: smalloc.c, line: 179Fatal 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 memoryI think i didnt made any error in file preparation and alteration of.itp and .top file. Because I tried it with2 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 toMemory of system if so what is the requirementfor making this run possible. I got struck up in my work I am highly in need of ur help...Thanks in advancewith regards,N.Hema Dhevi 
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