Re: [gmx-users] Re:gmx-users Digest, Vol 67, Issue 150 (memory allocationerror)

hema dhevi hema_gromacs at
Thu Dec 3 07:57:22 CET 2009

 hai justin, ya its robust. and urs is the only tutorial which i found for transmembrane protein MD simulation in GROMACS. Its really useful. thank you.As you said i tried it in other system also there i used gromacs version 3.3.3. i am getting the same kind of error.I didnt use any special configuration flags for installation, for both the versions and in both the systems.And the compiler which i am using isgcc version 4.1.2 20070626 (Red Hat 4.1.214)Thanks in advancewith regards N.Hema Dhevi Original message From:Justin A. Lemkul< jalemkul at >Date: 01 Dec 09 17:34:30Subject:Re: [gmxusers] Re:gmxusers Digest, Vol 67, Issue 150 (memory allocationerror)To: hema dhevi , Discussion list for GROMACS users hema dhevi wrote: >>> hai justin, >> ya i am working on actual KALP tutorial only >> >> and i am using the pdb file which is given in the website. This is > the first time i am 
 doing MD simulation > for transmembrane proteins before using the protein of my interest i > tried it with the peptide given the tutorial. >> hereby i am attaching the .mdp file which i am using >> ; minim.mdp  used as input into grompp to generate em.tpr > ; Parameters describing what to do, when to stop and what to save > integrator= steep; Algorithm (steep = steepest descent minimization) > emtol= 1000.0; Stop minimization when the maximum force < 1000.0 kJ/mol/nm > emstep= 0.01; Energy step size > nsteps= 50000; Maximum number of (minimization) steps to perform >> ; Parameters describing how to find the neighbors of each atom and ho >w to calculate the interactions > nstlist= 1; Frequency to update the neighbor list and long range forces > nstype= grid; Method to determine neighbor list (simple, grid) > rlist= 1.2; Cutoff for making neighbor list (short range forces) > coulombtype= PME; Treatment of long range electrostatic interactions > rcoulomb= 1.2; Shortrange electr
 ostatic cutoff > rvdw= 1.2; Shortrange Van der Waals cutoff > pbc= xyz ; Periodic Boundary Conditions (yes/no) >> Well, the KALP system is very robust (hence why I wrote the tutorial), so theproblem is likely coming from your machine.Do you have any other computer youcan try it on?Otherwise, post the commands you used to install Gromacs (anyspecial configuration flags, etc) as well as the compilers used (and versions)and any hardware details you can.Perhaps someone can spot the problem.Justin========================================Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILESIGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at] | (540) 2319080 
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