<br>hai justin, <br><br>ya its robust. and urs is the only tutorial which i found for transmembrane protein MD simulation in GROMACS. Its really useful. thank you.<br><br>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.<br>I didnt use any special configuration flags for installation, for both the versions and in both the <br>systems.<br><br>And the compiler which i am using is <span style="font-weight: bold;">gcc version 4.1.2 20070626 (Red Hat 4.1.2-14)<br><br><span style="font-weight: bold;">T</span></span>hanks in advance<br><br>with regards <br>N.Hema Dhevi<span style="font-weight: bold;"><span style="font-weight: bold;"><br></span></span><br><blockquote><br>---------- Original message ----------<br>From:Justin A. Lemkul< jalemkul@vt.edu ><br>Date: 01 Dec 09 17:34:30<br>Subject: Re: [gmx-users] Re:gmx-users Digest, Vol 67, Issue 150 (memory allocationerror)<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>
> <br>
> <br>
> hai justin,<br>
> <br>
> ya i am working on actual KALP tutorial only<br>
> <br>
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/index.html<br>
> <br>
> and i am using the pdb file which is given in the website. This is<br>
> the first time i am doing MD simulation<br>
> for transmembrane proteins before using the protein of my interest i<br>
> tried it with the peptide given the tutorial.<br>
> <br>
> hereby i am attaching the .mdp file which i am using<br>
> <br>
> ; minim.mdp - used as input into grompp to generate em.tpr<br>
> ; Parameters describing what to do, when to stop and what to save<br>
> integrator = steep Algorithm (steep = steepest descent minimization)<br>
> emtol = 1000.0 Stop minimization when the maximum force < 1000.0 kJ/mol/nm<br>
> emstep = 0.01 ; Energy step size<br>
> nsteps = 50000 Maximum number of (minimization) steps to perform<br>
> <br>
> ; Parameters describing how to find the neighbors of each atom and ho<br>
> w to calculate the interactions<br>
> nstlist = 1 Frequency to update the neighbor list and long range forces<br>
> ns_type = grid Method to determine neighbor list (simple, grid)<br>
> rlist = 1.2 Cut-off for making neighbor list (short range forces)<br>
> coulombtype = PME Treatment of long range electrostatic interactions<br>
> rcoulomb = 1.2 Short-range electrostatic cut-off<br>
> rvdw = 1.2 Short-range Van der Waals cut-off<br>
> pbc = xyz Periodic Boundary Conditions (yes/no)<br>
> <br>
> <br>
<br>
Well, the KALP system is very robust (hence why I wrote the tutorial), so the <br>
problem is likely coming from your machine. Do you have any other computer you <br>
can try it on? Otherwise, post the commands you used to install Gromacs (any <br>
special configuration flags, etc) as well as the compilers used (and versions) <br>
and any hardware details you can. Perhaps someone can spot the problem.<br>
<br>
-Justin<br>
<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<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>