Dear Gromacsers, This seems more suited to gmx-developers but as the original thread was on gmx-users, I'm posting it here.
Anyway, regarding the excessive memory usage of g_msd when using the -mol flag, as reported recently, I believe I've identified the source of the problem: the array of per-molecule MSD data in curr->lsq. In particular, it appears that the call to gmx_stats_add_point on line 476 is the key offender. I haven't the time at the moment to dig any further than this, unfortunately, but the attached patch (gmx_msd.mem.patch) may be of temporary use to users of g_msd. It merely comments out the call to gmx_stats_init and the printmol routine. If anybody wishes to retain the calculation of D for each individual molecule, they will need to recode the data accumulation in the style of that for the overall calculation I expect. There is also the problem of the large difference in the calculated results when using the -mol flag, as reported by Florian. I think the cause of this is an error in the logic within the corr_loop routine. The original sequence is: 1. If first iteration, copy current frame to previous 2. If -mol, make molecules whole 3. Remove PBC jumps 4. If -mol, calculate molecule COMs and copy to xa array I believe the correct order for this sequence should be 2, 4, 1, 3. The original order results in xa[prev] containing zero for every position on step 1 and also in the PBC step operating on an array that hasn't been repopulated yet, with the result that jumps are not removed correctly. I've tested the new sequence for a single PF6 molecule and for the corresponding P atom (which is almost exactly at the COM) and obtained very nearly identical results for each (which wasn't the case previously). I've attached a separate patch to reorder these function calls (gmx_msd.mol.patch). Both patches are for the v4.5.4 copy of gmx_msd.c, by the way. cheers, Simon =========================================== Dr. Simon Butler Theorie Physikaliche Chemie Eduard-Zintl-Institut Technische Universität Darmstadt Petersenstrasse 20 64287 Darmstadt Deutschland Tel: +49-6151-16 6537 Email: s.but...@theo.chemie.tu-darmstadt.de ===========================================
474a475,476 > /* disabled due to memory issues */ > /* 476a479 > */ 629c632 < curr->lsq[curr->nrestart-1][i] = gmx_stats_init(); --- > curr->lsq[curr->nrestart-1][i] = NULL; /* gmx_stats_init(); */ /* disabled due to memory issues */ 811c814 < printmol(msd,mol_file,pdb_file,index[0],top,x,ePBC,box,oenv); --- > /* printmol(msd,mol_file,pdb_file,index[0],top,x,ePBC,box,oenv); */ /* disabled due to memory issues */
664a682,689 > /* make the molecules whole */ > if (bMol) > gmx_rmpbc(gpbc,natoms,box,x[cur]); > > /* calculate the molecules' centers of masses and put them into xa */ > if (bMol) > calc_mol_com(gnx[0],index[0],&top->mols,&top->atoms, x[cur],xa[cur]); > 671,674d695 < /* make the molecules whole */ < if (bMol) < gmx_rmpbc(gpbc,natoms,box,x[cur]); < 689,692d709 < /* calculate the molecules' centers of masses and put them into xa */ < if (bMol) < calc_mol_com(gnx[0],index[0],&top->mols,&top->atoms, x[cur],xa[cur]); <
-- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
