Merge pull request #325 from carlocamilloni/main

added regtest of user provided pairs in make_mat

test/run_make_mat.sh

@@ -1,8 +1,13 @@
 set -e
 set -o pipefail
-tar -zxf test_inputs/make_mat/hh.tgz -C test_inputs/make_mat/
-python ../tools/make_mat/make_mat.py --histo test_inputs/make_mat/histo --target_top test_inputs/make_mat/topol_md.top --mego_top test_inputs/make_mat/topol_ref.top --cutoff 0.75 --inter --out  test_inputs/make_mat/
-python ../tools/make_mat/make_mat.py --histo test_inputs/make_mat/histo --target_top test_inputs/make_mat/topol_md.top --mego_top test_inputs/make_mat/topol_ref.top --cutoff 0.75 --out  test_inputs/make_mat/
-diff test_inputs/make_mat/intramat_1_1.ndx test_outputs/make_mat/intramat_1_1.ndx
-diff test_inputs/make_mat/intermat_1_1.ndx test_outputs/make_mat/intermat_1_1.ndx
+
+tar -zxf test_inputs/make_mat_ttr/hh.tgz -C test_inputs/make_mat_ttr/
+python ../tools/make_mat/make_mat.py --histo test_inputs/make_mat_ttr/histo --target_top test_inputs/make_mat_ttr/topol_md.top --mego_top test_inputs/make_mat_ttr/topol_ref.top --cutoff 0.75 --inter --out  test_inputs/make_mat_ttr/
+python ../tools/make_mat/make_mat.py --histo test_inputs/make_mat_ttr/histo --target_top test_inputs/make_mat_ttr/topol_md.top --mego_top test_inputs/make_mat_ttr/topol_ref.top --cutoff 0.75 --out  test_inputs/make_mat_ttr/
+diff test_inputs/make_mat_ttr/intramat_1_1.ndx test_outputs/make_mat_ttr/intramat_1_1.ndx
+diff test_inputs/make_mat_ttr/intermat_1_1.ndx test_outputs/make_mat_ttr/intermat_1_1.ndx
+
+tar -zxf test_inputs/make_mat_popc/hh.tgz -C test_inputs/make_mat_popc/
+python ../tools/make_mat/make_mat.py --histo test_inputs/make_mat_popc/histo --target_top test_inputs/make_mat_popc/topol_md.top --mego_top test_inputs/make_mat_popc/topol_ref.top --cutoff 0.75 --out  test_inputs/make_mat_popc/
+diff test_inputs/make_mat_popc/intramat_1_1.ndx test_outputs/make_mat_popc/intramat_1_1.ndx
 

test/test_inputs/make_mat_popc/topol_md.top

@@ -0,0 +1,20 @@
+;;
+;; Generated by CHARMM-GUI FF-Converter
+;;
+;; Correspondance:
+;; jul316@lehigh.edu or wonpil@lehigh.edu
+;;
+;; The main GROMACS topology file
+;;
+
+; Include forcefield parameters
+#include "toppar/forcefield.itp"
+#include "toppar/POPC.itp"
+
+[ system ]
+; Name
+POPC
+
+[ molecules ]
+; Compound	#mols
+POPC  	         1

test/test_inputs/make_mat_popc/topol_ref.top

@@ -0,0 +1,31 @@
+;
+;	File 'topol.top' was generated
+;	By user: gaia (1003)
+;	On host: monza
+;	At date: Tue Dec 19 11:41:49 2023
+;
+;	This is a standalone topology file
+;
+;	Created by:
+;	                    :-) GROMACS - gmx pdb2gmx, 2023.2 (-:
+;	
+;	Executable:   /mnt/data/software/gmx23_thread/bin/gmx
+;	Data prefix:  /mnt/data/software/gmx23_thread
+;	Working dir:  /home/gaia/multi-eGO_carlo/inputs/popc/reference
+;	Command line:
+;	  gmx pdb2gmx -f native.pdb -ignh
+;	Force field was read from current directory or a relative path - path added.
+;
+
+; Include forcefield parameters
+#include "../../../multi-ego-basic.ff/forcefield.itp"
+#include "../../../multi-ego-basic.ff/popc.itp"
+
+
+[ system ]
+; Name
+POPC
+
+[ molecules ]
+; Compound        #mols
+POPC            1

test/test_inputs/make_mat_popc/toppar/CLA.itp

@@ -0,0 +1,17 @@
+;;
+;; Generated by CHARMM-GUI FF-Converter
+;;
+;; Correspondance:
+;; jul316@lehigh.edu or wonpil@lehigh.edu
+;;
+;; GROMACS topology file for CLA
+;;
+
+
+[ moleculetype ]
+; name	nrexcl
+CLA	     1
+
+[ atoms ]
+; nr	type	resnr	residu	atom	cgnr	charge	mass
+     1        CLA     34      CLA    CLA      1    -1.000000    35.4500   ; qtot -1.000