change pbcatom default value into 0

HITS-MCM · Dec 21, 2020 · 520ed38 · 520ed38
1 parent 021deef
commit 520ed38
Show file tree

Hide file tree

Showing 3 changed files with 37 additions and 21 deletions.
diff --git a/docs/user-guide/mdp-options.rst b/docs/user-guide/mdp-options.rst
@@ -2180,12 +2180,12 @@ applied to a molecule in the system.
 
 .. mdp:: ramd-group1-receptor-pbcatom
 
-   (1)
+   (0)
    The value will be forwarded to the associated pull group of the receptor.
 
 .. mdp:: ramd-group1-ligand-pbcatom
 
-   (1)
+   (0)
    The value will be forwarded to the associated pull group of the ligand.
 
 .. mdp:: ramd-pbc-ref-prev-step-com

diff --git a/src/gromacs/gmxpreprocess/readramd.cpp b/src/gromacs/gmxpreprocess/readramd.cpp
@@ -62,12 +62,12 @@ void read_ramdparams(std::vector<t_inpfile>* inp, gmx::RAMDParams* ramdparams, w
         inp->emplace_back(0, 1, false, false, false, pull1_prefix + "-name",
             get_estr(inp, ramd_prefix + "-receptor", "Protein"));
         inp->emplace_back(0, 1, false, false, false, pull1_prefix + "-pbcatom",
-            get_estr(inp, ramd_prefix + "-receptor-pbc-atom", "1"));
+            get_estr(inp, ramd_prefix + "-receptor-pbc-atom", "0"));
 
         inp->emplace_back(0, 1, false, false, false, pull2_prefix + "-name",
             get_estr(inp, ramd_prefix + "-ligand", "INH"));
         inp->emplace_back(0, 1, false, false, false, pull2_prefix + "-pbcatom",
-            get_estr(inp, ramd_prefix + "-ligand-pbc-atom", "1"));
+            get_estr(inp, ramd_prefix + "-ligand-pbc-atom", "0"));
 
         ramdgrp->force = get_ereal(inp, ramd_prefix + "-force", 600, wi);
         ramdgrp->r_min_dist = get_ereal(inp, ramd_prefix + "-r-min-dist", 0.0025, wi);

diff --git a/src/programs/mdrun/tests/ramd.cpp b/src/programs/mdrun/tests/ramd.cpp
@@ -38,7 +38,7 @@ TEST_F(RAMDTest, RAMD_1whhi)
     runner_.useTopGroAndNdxFromDatabase("1wdhi");
     const std::string mdpContents = R"(
         dt                       = 0.004
-        nsteps                   = 2
+        nsteps                   = 4
         tcoupl                   = Berendsen
         tc-grps                  = System
         tau-t                    = 0.5
@@ -53,8 +53,10 @@ TEST_F(RAMDTest, RAMD_1whhi)
         ramd-group1-force        = 600.0
         ramd-group1-r-min-dist   = 0.025
         ramd-group1-max-dist     = 4.0
-        ramd-eval-freq           = 50
-        ramd-force-out-freq      = 0
+        ramd-eval-freq           = 2
+        ramd-force-out-freq      = 2
+        ramd-group1-ligand-pbcatom   = 1631
+        ramd-group1-receptor-pbcatom = 3289
     )";
     runner_.useStringAsMdpFile(mdpContents);
 
@@ -69,7 +71,7 @@ TEST_F(RAMDTest, RAMD_membrane)
     runner_.useTopGroAndNdxFromDatabase("membrane");
     const std::string mdpContents = R"(
         dt                       = 0.004
-        nsteps                   = 2
+        nsteps                   = 4
         tcoupl                   = Berendsen
         tc-grps                  = System
         tau-t                    = 0.5
@@ -84,8 +86,10 @@ TEST_F(RAMDTest, RAMD_membrane)
         ramd-group1-force        = 600.0
         ramd-group1-r-min-dist   = 0.025
         ramd-group1-max-dist     = 4.0
-        ramd-eval-freq           = 50
-        ramd-force-out-freq      = 0
+        ramd-eval-freq           = 2
+        ramd-force-out-freq      = 2
+        ramd-group1-ligand-pbcatom   = 3255
+        ramd-group1-receptor-pbcatom = 6580
     )";
     runner_.useStringAsMdpFile(mdpContents);
 
@@ -102,10 +106,10 @@ TEST_F(RAMDTest, RAMD_hsp90)
     const std::string mdpContents = R"(
         integrator               = md
         dt                       = 0.002
-        nsteps                   = 200
-        nstlog                   = 2500
-        nstenergy                = 2500
-        nstxout-compressed       = 500
+        nsteps                   = 4
+        nstlog                   = 1
+        nstenergy                = 1
+        nstxout-compressed       = 1
         continuation             = yes
         constraints              = h-bonds
         constraint-algorithm     = lincs
@@ -150,8 +154,10 @@ TEST_F(RAMDTest, RAMD_hsp90)
         ramd-group1-force        = 585.0
         ramd-group1-r-min-dist   = 0.0025
         ramd-group1-max-dist     = 4.0
-        ramd-eval-freq           = 60
+        ramd-eval-freq           = 2
         ramd-force-out-freq      = 0
+        ramd-group1-ligand-pbcatom   = 1
+        ramd-group1-receptor-pbcatom = 1
     )";
     runner_.useStringAsMdpFile(mdpContents);
 
@@ -167,10 +173,10 @@ TEST_F(RAMDTest, RAMD_GlyR)
     const std::string mdpContents = R"(
         integrator               = md
         dt                       = 0.002
-        nsteps                   = 100
-        nstlog                   = 1000
-        nstenergy                = 1000
-        nstxout-compressed       = 1000
+        nsteps                   = 4
+        nstlog                   = 1
+        nstenergy                = 1
+        nstxout-compressed       = 1
         continuation             = yes
         constraints              = h-bonds
         constraint-algorithm     = lincs
@@ -216,9 +222,19 @@ TEST_F(RAMDTest, RAMD_GlyR)
         ramd-group5-force        = 600
         ramd-group5-max_dist     = 40.0
         ramd-group5-r_min_dist   = 0.0025
-        ramd-eval_freq           = 50
-        ramd-force_out_freq      = 100
+        ramd-eval_freq           = 2
+        ramd-force_out_freq      = 2
         ramd-old-angle-dist      = no
+        ramd-group1-ligand-pbcatom   = 0
+        ramd-group1-receptor-pbcatom = 2692
+        ramd-group2-ligand-pbcatom   = 0
+        ramd-group2-receptor-pbcatom = 8075
+        ramd-group3-ligand-pbcatom   = 0
+        ramd-group3-receptor-pbcatom = 13458
+        ramd-group4-ligand-pbcatom   = 0
+        ramd-group4-receptor-pbcatom = 18841
+        ramd-group5-ligand-pbcatom   = 0
+        ramd-group5-receptor-pbcatom = 24224
     )";
     runner_.useStringAsMdpFile(mdpContents);