new upload

README

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+

README.md

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+
+# Na-Cl Interaction Testing for NBFIX and NBTHOLE
+
+This folder contains scripts and resources for testing the NBFIX and NBTHOLE parameters for Na-Cl interactions.
+
+## Contents
+
+- **`run_charmm.sh`**: Script to run the CHARMM test.
+- **`run_openmm.sh`**: Script to run the OpenMM test.
+- **`bench_mark`**: Folder containing benchmark data for performance and accuracy comparisons.
+
+## How to Run the Tests
+
+To execute the tests, follow these steps:
+
+1. Ensure all required dependencies for CHARMM and OpenMM are installed.
+2. Make the scripts executable:
+   ```bash
+   chmod +x run_charmm.sh run_openmm.sh
+   ```
+3. Run the CHARMM and OpenMM tests with the following commands:
+
+   ```bash
+   ./run_charmm.sh
+   ./run_openmm.sh
+   ```
+
+Alternatively, you can use the `run_tests.sh` script (if available) to automatically run both tests and log the output.
+
+## Viewing Benchmark Results
+
+The `bench_mark` folder contains benchmark data for comparison. After running the tests, compare the outputs with these benchmarks to assess accuracy and performance.
+
+---
+
+This `README.md` gives a clear overview of the project structure and instructions on how to run and review tests. Let me know if you'd like any additional customization!

bench_mark

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+Printing Energy Components for Na-Cl system 
+Distance (A),  Total Energy (kcal/mol)
+2.8 -69.629
+
+BOND 0.0
+ANGL 0.0
+DIHE 0.0
+UREY 0.0
+IMPR 0.0
+CMAP 0.0
+VDW  3.568
+ELE  -73.636
+DRUD 0.438
+OTH1 0.0
+TOTE -69.629

charmm_test/ener_ljpme.inp

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+* ion interaction energy surface
+*
+
+iofo exte
+
+stream ../drude_toppar_nbfix_nbthole_test/toppar_drude_water_nacl.str
+
+
+set ion  SOD 
+set resi CLA
+
+
+    set xnew = 2.8
+
+
+    open read unit 10 card name ./sod_cla_drude.psf
+    read psf unit 10 card
+
+    open read unit 10 card name ../coords/@ion_@resi_@xnew_min.pdb
+    read coor unit 10 pdb resid
+    close unit 10
+
+
+    !stop 
+
+    set x 200.
+    set y @x
+    set z @x
+    crystal define cubic @x @y @z 90. 90. 90.
+    crystal build cutoff 10. noper 0
+
+fast off ! for ljpme
+
+set fftx = 360
+set ffty = 360
+set fftz = 360
+
+set dk = 0.4
+nbonds atom vatom vswitch bycb -
+       ctonnb 9.0 ctofnb 8.0 cutnb 13.5 cutim 13.5 -
+       inbfrq -1 imgfrq -1 wmin 1.0 cdie eps 1.0 -
+       ewald pmew fftx @fftx ffty @ffty fftz @fftz  kappa .34 spline order 6 -
+       dpme dkappa @dk dftx @fftx dfty @fftx dftz @fftx dorder 6
+energy
+
+set bonds    ?BOND
+set angle    ?ANGL
+set dihedral ?DIHE
+set urey     ?UREY
+set improper ?IMPR
+set cmap     ?CMAP
+set vdw      ?VDW
+set elec     ?ELEC
+set ewks     ?EWKS
+set ewex     ?EWEX
+set ewse     ?EWSE
+
+calc ele = @ewks + @ewex + @ewse + @elec
+set tote   ?ENER
+
+open write unit 99 card name ../Output_CHARMM_ljpme.out
+
+write title unit 99
+* Printing Energy Components for Na-Cl system ljpme
+* Distance (A),  Total Energy (kcal/mol)
+* @xnew  @tote
+* i   
+* BOND @bonds
+* ANGL @angle
+* DIHE @dihedral
+* UREY @urey
+* IMPR @improper
+* CMAP @cmap
+* VDW  @vdw
+* ELE  @ele
+* DRUD :reflects in bonded interaction in charmm
+* OTH1 
+* TOTE @tote
+*
+
+
+
+
+stop
+
+