From: Roland Schulz <roland@utk.edu>
Date: Thu, 22 May 2014 22:16:13 +0000 (-0400)
Subject: Fix memory issue in solvate
X-Git-Url: http://biod.pnpi.spb.ru/gitweb/?a=commitdiff_plain;h=d77dddb83f64f0265b8f226ff1061b37bc10877b;p=alexxy%2Fgromacs.git

Fix memory issue in solvate

Caused by SIMD padding introduced by new group kernels.

Fixes #1499

Change-Id: I5126217c9b752f1c1fd04d01e2644987fdc52d5b
---

diff --git a/src/tools/addconf.c b/src/tools/addconf.c
index 0df691f0b3..448d7955d0 100644
--- a/src/tools/addconf.c
+++ b/src/tools/addconf.c
@@ -431,6 +431,11 @@ 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 */