Update advice about grompp -t

[alexxy/gromacs.git] / src / gromacs / gmxpreprocess / grompp.c

diff --git a/src/gromacs/gmxpreprocess/grompp.c b/src/gromacs/gmxpreprocess/grompp.c
index b63ce1020f3155bbc7d11f9c3754c3e81b792767..0983650920dc88dc5cccafcd9ef21d8910183fa8 100644 (file)
--- a/src/gromacs/gmxpreprocess/grompp.c
+++ b/src/gromacs/gmxpreprocess/grompp.c
@@ -1374,7 +1374,7 @@ static void set_verlet_buffer(const gmx_mtop_t *mtop,
                             &ls, &n_nonlin_vsite, &rlist_1x1);
 
     /* Set the pair-list buffer size in ir */
-    verletbuf_get_list_setup(FALSE, &ls);
+    verletbuf_get_list_setup(FALSE, FALSE, &ls);
     calc_verlet_buffer_size(mtop, det(box), ir, buffer_temp,
                             &ls, &n_nonlin_vsite, &ir->rlist);
 
@@ -1392,6 +1392,8 @@ static void set_verlet_buffer(const gmx_mtop_t *mtop,
            ls.cluster_size_i, ls.cluster_size_j,
            ir->rlist, ir->rlist-max(ir->rvdw, ir->rcoulomb));
 
+    printf("Note that mdrun will redetermine rlist based on the actual pair-list setup\n");
+
     if (sqr(ir->rlistlong) >= max_cutoff2(ir->ePBC, box))
     {
         gmx_fatal(FARGS, "The pair-list cut-off (%g nm) is longer than half the shortest box vector or longer than the smallest box diagonal element (%g nm). Increase the box size or decrease nstlist or increase verlet-buffer-tolerance.", ir->rlistlong, sqrt(max_cutoff2(ir->ePBC, box)));
@@ -1474,7 +1476,9 @@ int gmx_grompp(int argc, char *argv[])
         "with [TT]-cpi[tt]. If you wish to change the ensemble or things",
         "like output frequency, then supplying the checkpoint file to",
         "[THISMODULE] with [TT]-t[tt] along with a new [TT].mdp[tt] file",
-        "with [TT]-f[tt] is the recommended procedure.[PAR]",
+        "with [TT]-f[tt] is the recommended procedure. Actually preserving",
+        "the ensemble (if possible) still requires passing the checkpoint",
+        "file to [gmx-mdrun] [TT]-cpi[tt].[PAR]",
 
         "By default, all bonded interactions which have constant energy due to",
         "virtual site constructions will be removed. If this constant energy is",