Merge release-5-0 into master

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

diff --git a/src/gromacs/gmxpreprocess/addconf.c b/src/gromacs/gmxpreprocess/addconf.c
index 1ad661eacb6854b8fb59aad470797451e196962c..e89b0bbb311123e7d7679bc96645a48575f4e184 100644 (file)
--- a/src/gromacs/gmxpreprocess/addconf.c
+++ b/src/gromacs/gmxpreprocess/addconf.c
@@ -439,6 +439,11 @@ void add_conf(t_atoms *atoms, rvec **x, rvec **v, real **r, gmx_bool bSrenew,
             for (j = j0; (j < j1 && nremove < natoms_solvt); j++)
             {
                 jnr = nlist->jjnr[j];
+                if (jnr < 0)
+                {
+                    /* skip padding */
+                    continue;
+                }
                 copy_rvec(x_all[jnr], xj);
 
                 /* Check solvent-protein and solvent-solvent */