PAUL NEWMAN wrote: > PAUL NEWMAN wrote: > > Dear all: > > I made a simulation about a polyelectrolyte with some ions, it runs ok > > when I use cut-off for both Wdv and Coulomb. However I get the following > > error when I change it to PME. I attache my mdp file . Could someone > > help me to find what it's wrong in my file?. Thanks in advance. > > ------------------------------------------------------- > > Program mdrun, VERSION 3.3.1 > > Source code file: fftgrid.c, line: 75 > > > > Fatal error: > > Failed to allocated u bytes of aligned memory. > > ------------------------------------------------------- > > CARSTEN wrote: > >How big is your system (number of atoms)? Seems there is not enough > >memory to initialise the pme grid. On how many CPUs and on how many > >nodes do you run? > >Carsten > > Thanks Carsten for replying so fast. In my simulation I consider a > single polyelectrolyte chain consisting of 50 charged beads of valency > -1 with 50 oppositely charged counterions of same valency so my system > is 100 atoms. My box simulation is 400 nm x 400 nm x 400 nm and the > polyelectrolyte length is 100 nm. I'm runnig in a single processor. I > think my system is small, isn't it?
Hi Paul, with a box size of 400nm^3 and a standard fourierspacing (= maximum distance between the pme grid points) of 0.12 nm you end up with a pme grid of 3334^3 points which is HUGE, so you run out of memory. (A typical pme grid for a 100000 atom water system will have around 100^3 pme grid points.) If you do not need periodic boundary conditions (?) you could switch them off and also pme and then explicitly calculate all coulomb interactions, which should be fast with 100 atoms. I think you have to set rlist=nstlist=0 for explicit coulomb calculation. Carsten > I can send you all my files if you want. Any suggestion would be > highly appreciated and thanks in advance. > > Cheers, > > Paul > National Tsing Hua University (清�A大�W) > > �x�x你的�兔� > I appreciate your help. Thanks! > Os agradezco la ayuda. Gracias! > > > ------------------------------------------------------------------------ > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Department Am Fassberg 11 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/research/dep/grubmueller/ http://www.gwdg.de/~ckutzne _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
