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simulating_hydrocarbon_mixtures

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simulating_hydrocarbon_mixtures [2018/01/12 16:59] – editsimulating_hydrocarbon_mixtures [2018/05/31 14:13] (current) – admin
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-**(Page is under construction. Editing in progress)** 
  
-**(The files mention below can be found at https://drive.google.com/open?id=1qmC5TQ3FDq8wyrmsUgUDqWiH1e87Yflt )**+**(The files mention below can be found at here {{instructions_manual.zip}} )**
  
 **__A) Generating the required files for a molecule (Example: Cyclohexane)__** **__A) Generating the required files for a molecule (Example: Cyclohexane)__**
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-**__C) How to Access Deep Thought 1 (DT1)__**+**__C) How to Access Deepthought2 (DT2)__**
  
  1. Download WinSCP from https://winscp.net/eng/download.php \\   1. Download WinSCP from https://winscp.net/eng/download.php \\ 
  -- WinSCP allows you to upload files to and download files from Deep Thought 1 \\  -- WinSCP allows you to upload files to and download files from Deep Thought 1 \\
  2. Open WinSCP and log-in using: \\  2. Open WinSCP and log-in using: \\
-    Host name: login.deepthought.umd.edu +    Host name: login.deepthought2.umd.edu 
     Port number: 22      Port number: 22 
     User name: universityID             <- this is your university id (not id number)      User name: universityID             <- this is your university id (not id number) 
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  -- Putty allows you to access Deep Thought 1 via a console and execute scripts \\  -- Putty allows you to access Deep Thought 1 via a console and execute scripts \\
  5. Open Putty and log-in using: \\  5. Open Putty and log-in using: \\
-    Host Name: login.deepthought.umd.edu +    Host Name: login.deepthought2.umd.edu 
     Port: 22      Port: 22 
     Click “Open”      Click “Open” 
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  -- When you first login, you will be in the “lustre/home/universityID” folder on the server.\\  -- When you first login, you will be in the “lustre/home/universityID” folder on the server.\\
  6. Type “source startup.csh” to execute the script you previously uploaded \\  6. Type “source startup.csh” to execute the script you previously uploaded \\
-** -- The previous step must be done every time you login into DT1** \\+** -- The previous step must be done every time you login into DT2** \\
  -- The startup.csh script assigns the location of the 2 programs: Packmol and CHARMM to the environment variables “$packmol” and “$charmm”, respectively. This will ease the execution of future scripts. \\  -- The startup.csh script assigns the location of the 2 programs: Packmol and CHARMM to the environment variables “$packmol” and “$charmm”, respectively. This will ease the execution of future scripts. \\
     (see startup.csh)     (see startup.csh)
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 **__D) Packing a Mixture of Water and Cyclohexane__** **__D) Packing a Mixture of Water and Cyclohexane__**
  
- 1. In WinSCP, navigate to “lustre/universityID” on DT1 and create a folder called “packing” \\+ 1. In WinSCP, navigate to “lustre/universityID” on DT2 and create a folder called “packing” \\
  -- (to create a folder, look for the   icon on the right side of the screen) \\  -- (to create a folder, look for the   icon on the right side of the screen) \\
- 2. Transfer “cyclohexane/cyclohexane2.pdb” and “water/water.pdb” to this folder on DT1 \\ + 2. Transfer “cyclohexane/cyclohexane2.pdb” and “water/water.pdb” to this folder on DT2 \\ 
- 3. Transfer the packmol script “packing/packing.inp” to the “packing” folder on DT1 \\+ 3. Transfer the packmol script “packing/packing.inp” to the “packing” folder on DT2 \\
  4. The packmol script is explained via comments inside the file. \\  4. The packmol script is explained via comments inside the file. \\
  5. In Putty, navigate to “lustre/universityID/packing” \\  5. In Putty, navigate to “lustre/universityID/packing” \\
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     chmod 700 packing.inp     chmod 700 packing.inp
     $packmol < packing.inp > packing.out     $packmol < packing.inp > packing.out
- -- This should result in two new files being generated in the “packing” folder on DT1  \\+ -- This should result in two new files being generated in the “packing” folder on DT2  \\
  -- (you might need to Refresh   to see the new files) \\  -- (you might need to Refresh   to see the new files) \\
  -- One of the files will be called “packing.out” which outlines the progress of Packmol as it packs the mixture. The other file will be called “mixture.pdb” which will contain the packed mixture. If the “mixture.pdb” file was not generated, then an error occurred while packing. You will need to read “packing.out” to understand and correct the error.  \\  -- One of the files will be called “packing.out” which outlines the progress of Packmol as it packs the mixture. The other file will be called “mixture.pdb” which will contain the packed mixture. If the “mixture.pdb” file was not generated, then an error occurred while packing. You will need to read “packing.out” to understand and correct the error.  \\
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 -- Now that we have packed the mixture, the next step is to generate a .psf file for the mixture. This .psf file “contains all of the molecule-specific information needed to apply a particular force field to a molecular system”(http://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-unix-html/node23.html). We will use CHARMM to generate this file. \\ -- Now that we have packed the mixture, the next step is to generate a .psf file for the mixture. This .psf file “contains all of the molecule-specific information needed to apply a particular force field to a molecular system”(http://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-unix-html/node23.html). We will use CHARMM to generate this file. \\
  
- 1. In WinSCP, navigate to “lustre/universityID” on DT1 and create a folder called “generatingPSF”. \\+ 1. In WinSCP, navigate to “lustre/universityID” on DT2 and create a folder called “generatingPSF”. \\
  2. In WinSCP, drag the following into the “generatingPSF” folder: \\  2. In WinSCP, drag the following into the “generatingPSF” folder: \\
     water/top_tip4p_2005.rtf     water/top_tip4p_2005.rtf
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     chmod 700 generatingPSF.inp     chmod 700 generatingPSF.inp
     $charmm < generatingPSF.inp > generatingPSF.out     $charmm < generatingPSF.inp > generatingPSF.out
-     + -- This should result in three new files being generated in the “generatingPSF” folder on DT2: \\
- -- This should result in three new files being generated in the “generatingPSF” folder on DT1: \\+
  -- (if this is not the case, check the generatingPSF.out file to understand and correct any errors) \\  -- (if this is not the case, check the generatingPSF.out file to understand and correct any errors) \\
     mixture_charmm.pdb         <- coordinates of our mixture generated by CHARMM     mixture_charmm.pdb         <- coordinates of our mixture generated by CHARMM
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 __First, let’s run the short (1ns) simulation:__ \\  __First, let’s run the short (1ns) simulation:__ \\ 
  
- 1. In WinSCP, navigate to “lustre/universityID” on DT1 and create a folder called “runningSim”. \\ + 1. In WinSCP, navigate to “lustre/universityID” on DT2 and create a folder called “runningSim”. \\ 
  2. In this folder, create another folder called “equalize”. \\   2. In this folder, create another folder called “equalize”. \\ 
  3. In WinSCP, drag the following into the “equalize” folder: \\   3. In WinSCP, drag the following into the “equalize” folder: \\ 
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     generatingPSF/mixture_charmm.psf     generatingPSF/mixture_charmm.psf
     runningSim/equalize/runningSim.inp                     <- NAMD input script with simulation parameters     runningSim/equalize/runningSim.inp                     <- NAMD input script with simulation parameters
-    runningSim/equalize/slurmInstructions.csh              <- Instructions for Slurm to run your simulation on DT1+    runningSim/equalize/slurmInstructions.csh              <- Instructions for Slurm to run your simulation on DT2
  -- (these should be the only files in the “equalize” folder before submitting the job to Slurm) \\   -- (these should be the only files in the “equalize” folder before submitting the job to Slurm) \\ 
  -- (See comments inside “runningSim.inp” and “slurmInstructions.csh”) \\   -- (See comments inside “runningSim.inp” and “slurmInstructions.csh”) \\ 
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     sbatch -A energybio-hi slurmInstructions.csh     sbatch -A energybio-hi slurmInstructions.csh
  -- If the job submission is successful, you should see “Submitted batch job ######” in the console. \\   -- If the job submission is successful, you should see “Submitted batch job ######” in the console. \\ 
- -- To view all jobs that you are running on DT1, type “squeue -u universityID” into the console. \\ + -- To view all jobs that you are running on DT2, type “squeue -u universityID” into the console. \\ 
  
 __Tracking your simulation:__  \\  __Tracking your simulation:__  \\ 
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 -- The file “runningSim.out” will be generated in the “equalize” folder that will outline the progress of the simulation. After all the files have been read and the simulation has begun, you will start to see estimates of time remaining until the simulation is complete in “runningSim.out”. A few other files will be generated as well. The file that will allow you to watch the progression of your simulation is the .dcd file. Snapshots of your system are taken periodically and added to this dcd file. While the simulation is running, the dcd file should be increasing in size. To view these snapshots, we will use VMD:  -- The file “runningSim.out” will be generated in the “equalize” folder that will outline the progress of the simulation. After all the files have been read and the simulation has begun, you will start to see estimates of time remaining until the simulation is complete in “runningSim.out”. A few other files will be generated as well. The file that will allow you to watch the progression of your simulation is the .dcd file. Snapshots of your system are taken periodically and added to this dcd file. While the simulation is running, the dcd file should be increasing in size. To view these snapshots, we will use VMD: 
  
- 6. Transfer “runningSim/equalize/mixture_prod.dcd” from DT1 to your machine \\ + 6. Transfer “runningSim/equalize/mixture_prod.dcd” from DT2 to your machine \\ 
- 7. Transfer “runningSim/equalize/mixture_charmm.psf” from DT1 to your machine \\ + 7. Transfer “runningSim/equalize/mixture_charmm.psf” from DT2 to your machine \\ 
  8. Open VMD \\  8. Open VMD \\
  9. Click File > New Molecule… > Browse > navigate to and select “mixture_charmm.psf” > Ok > Load \\  9. Click File > New Molecule… > Browse > navigate to and select “mixture_charmm.psf” > Ok > Load \\
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  -- Once your equilibrium simulation is complete, you can begin to run extended simulations on your mixture. \\   -- Once your equilibrium simulation is complete, you can begin to run extended simulations on your mixture. \\ 
  
-__Running Extended Simulations__  \\+__Running Extended Simulations:__  \\
  
-11. In WinSCP, navigate to the “runningSim” folder on DT1 and create a folder called “sim1”. \\ +11. In WinSCP, navigate to the “runningSim” folder on DT2 and create a folder called “sim1”. \\ 
 12. In WinSCP, drag the following into the “sim1” folder: \\ 12. In WinSCP, drag the following into the “sim1” folder: \\
-     
     runningSim/equalize/mixture_prod.coor     runningSim/equalize/mixture_prod.coor
     runningSim/equalize/mixture_prod.vel     runningSim/equalize/mixture_prod.vel
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     runningSim/equalize/mixture_charmm.psf     runningSim/equalize/mixture_charmm.psf
     runningSim/sim1/slurmInstructions1.csh          <- slightly different for an extended simulation     runningSim/sim1/slurmInstructions1.csh          <- slightly different for an extended simulation
-    runningSim/sim1/runningSim1.inp                 <- Contains NAMD parameters for an extended simulation +    runningSim/sim1/runningSim1.inp                 <- Contains NAMD parameters for an extended simulation which differ from parameters for the equilibrium simulation
-                        which differ from parameters for the equilibrium simulation +
  -- (See comments inside “runningSim.inp” and “slurmInstructions.csh”) \\  -- (See comments inside “runningSim.inp” and “slurmInstructions.csh”) \\
  -- The process for submitting a job is the same:  \\  -- The process for submitting a job is the same:  \\
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 13. In Putty, navigate to “lustre/universityID/runningSim/sim1” \\ 13. In Putty, navigate to “lustre/universityID/runningSim/sim1” \\
 14. To submit your job to Slurm, type the following into the console:  \\ 14. To submit your job to Slurm, type the following into the console:  \\
-     
     dos2unix slurmInstructions1.csh     dos2unix slurmInstructions1.csh
     chmod 700 slurmInstructions1.csh     chmod 700 slurmInstructions1.csh
     sbatch -A energybio-hi slurmInstructions1.csh     sbatch -A energybio-hi slurmInstructions1.csh
- 
  -- If the job submission is successful, you should see “Submitted batch job ######” in the console.  \\  -- If the job submission is successful, you should see “Submitted batch job ######” in the console.  \\
- -- To view all jobs that you are running on DT1, type “squeue -u universityID” into the console. \\+ -- To view all jobs that you are running on DT2, type “squeue -u universityID” into the console. \\
  
 -- Once the first simulation finishes running, you transfer the output the “.coor”,”.vel” and “.xsc” files generated by this simulation to a new folder, along with the other necessary files. You must tweek "runningSim1.inp" and "slurmInstructions1.csh" to account for the different file input and output names and then you run the extended simulation again. I’ve included an example of this process in the “runningSim/sim2” folder. Review the files “runningSim2.inp” and “slurmInstructions2.inp” to see the tweeks that must be made to start this simulation from where the first simulation ended. \\ -- Once the first simulation finishes running, you transfer the output the “.coor”,”.vel” and “.xsc” files generated by this simulation to a new folder, along with the other necessary files. You must tweek "runningSim1.inp" and "slurmInstructions1.csh" to account for the different file input and output names and then you run the extended simulation again. I’ve included an example of this process in the “runningSim/sim2” folder. Review the files “runningSim2.inp” and “slurmInstructions2.inp” to see the tweeks that must be made to start this simulation from where the first simulation ended. \\
simulating_hydrocarbon_mixtures.1515794341.txt.gz · Last modified: 2018/01/12 16:59 by edit