View source for NAMD on Seawulf

Sample tcsh script for running NAMD

 #!/bin/tcsh
 #PBS -l nodes=8:ppn=2
 #PBS -l walltime=02:00:00
 
 set path = ( $path /usr/local/pkg/NAMD_2.6/Linux-amd64-MPI )
 setenv LD_LIBRARY_PATH "/usr/local/pkg/openmpi/lib:/lib:/usr/local/pkg/torque/lib/"
 set workdir = /home/sudipto/path/to/files
 cd $workdir
 set namd2 = /usr/local/pkg/NAMD_2.6/Linux-amd64-MPI/namd2
 
 mpirun -x PATH -x LD_LIBRARY_PATH -np 16 $namd2 01mi.in > 01mi.out

Use "qsub" to run the script above, info for the command on seawulf [http://ringo.ams.sunysb.edu/index.php/PBS_Queue PBS_queue]

==Running NAMD with AMBER parm and crd files==

NAMD will run systems prepared by AMBER. Here is a generic input file for doing this. for further details about each parameter, look in the NAMD User Guide. There are several parameters with dummy values such as Z-AMBERPARM or Z_AMBERCRD. Replace these placeholders with your filenames and other parameters. Anything in the NAMD input file with a # sign in front of it is interpreted as a comment. You need to uncomment the parameters you are using to create a valid input file from the generic one provided below. The cellbasisvectors and cellorigin parameters can be measured using VMD.

 #input files (section 3.2.1)
 amber                   on            #specifies we are using AMBER Prm and CRD files
 #parmfile Z-AMBERPARM                 #specifies we are using AMBER Prm and CRD files
 #ambercoor Z-AMBERCRD                 #specifies we are using AMBER Prm and CRD files
 #velocities Z-VELOCITIES              #velocity file for a restart note that in a restart delete the temp
 
 #output file (section 3.2.2)
 #outputname Z-OUTPUTNAME              #specifies the prefix for the output files
 binaryoutput            no            #activates binary output (yes=binary)
 DCDfreq                 1000          #number of timesteps between the writing coordinates
 
 #standard output (section 3.2.3)
 outputenergies          1000          #number of timesteps between energy output
 outputTiming            1000          #number of timesteps between timing output 
 
 #timestep parameters (section 5.3.1)
 firsttimestep           0             #frame number where the simulation starts
 timestep                1             #length of each step in fs
 stepspercycle           20            #how often the interacting particle lists are updated 
 
 #space partitionin (section 5.3.2)
 cutoff                  12            #non-bonded cutoff
 switching               on            #smoothing function for ES and VDW
 switchdist              10            #distance at which the smoothing function is applied
 pairlistdist            16            #distance >= switchdist for atom pairs to be included in the pairlist
 margin                  8             #see section 5.3.2
  
 #basic dynamics (section 5.3.3)
 exclude                 scaled1-4     #which bonded atom pairs are excluded from non-bonded calculations
 #temperature Z-TEMPERATURE            #INITIAL temperature of the simulation note delete on restart
 1-4scaling              0.833333      #1.0 for Charmm, 0.833333 for Amber
 scnb                    2             #This is default for both Amber and Charmm
 rigidbonds              water         #controls how shake is used
 rigidTolerance          0.00001       #allowable bond length error for shake
 
 #PME parameters (section 5.3.5)
 PME                     yes           #turns PME on or off (yes=on no=off)
 PMEGridSpacing          1.0           #standard spacing.  Namd asigns the grid size. 
 
 #constraints (section 6.1)
 constraints             on            #on or off
 #consref Z-CONSREF                    #pdb file with restraint reference positions
 #conskfile Z-CONSKFILE                #pdb file with force constant values
 conskcol                B             #use the beta column in the pdb for contraints
 
 #temperature control and equilibration (section 6.3)
 langevin                on            #turns langevin dynamics on or off
 langevinTemp            310           #temp to which langevin dynamics will be adjusted
 langevinDamping         1             #damping coefficient for langevin dynamics
 
 #periodic boundry conditions (section 6.4.3)
 cellbasisvector1 $boxsize_x 0 0       #defines the first periodic boundary
 cellbasisvector2 0 $boxsize_y 0       #defines the second periodic boundary
 cellbasisvector3 0 0 $boxsize_z       #defines the third periodic boundary
 cellorigin $centerofbox               #defines the xyz location of the center of the box
 
 #extendedSystem Z-EXTENDEDSYSTEM      #defines file which contains the PBC info from previous runs
 wrapwater               on            #wraps the waters to one box.
 wrapall                 on            #wraps every contiguous cluster of bonded atoms
 wrapNearest             off           #wraps coordinates to the nearest image to the origin
 
 #pressure control (section 6.5)
 langevinPiston          on            #turns on constant pressure
 langevinPistonTarget    1.01325       #target pressure
 langevinPistonPeriod    200           #period over which the pressure is averaged in fs
 langevinPistonDecay     100           #damping time scale in fs
 langevinPistonTemp      310           #should be equal to langevin temp 
 
 #equilibration
 #run Z-NSTEPS
 #minimize Z-NSTEPS

There are more details about running NAMD in the [[NAMD tutorial]], although the NAMD input files in that article are NOT up to date. Please use the input file from this article.

If you need to fine-tune your input files, it might take a long time if you hvae to submit jobs to the queue every time. For this reason, we have compiled a serial version of namd as well. This is in /usr/local/pkg/NAMD_2.6/Linux-amd64-g++

Only use that binary for testing (or serial jobs on the queue). Do not use that binary to run on the seawulf headnode for more than a few minutes.

==Running namd with psf and pdb inputs==

 #input files (section 3.2.1)
 #coordinates Z-COORDINATES             #name of coordinate (pdb) file
 #structure Z-STRUCTURE                 #psf file
 parameters par_all27_prot_lipid.prm    #parameter file
 paratypecharmm          on             #specifies if this is a charmm force field (on or off)
 #velocities Z-VELOCITIES               #velocity file for a restart. In a restart delete the temperature
 
 #output file (section 3.2.2)
 #outputname Z-OUTPUTNAME               #specifies the prefix for the output files
 binaryoutput            no             #activates binary output (yes=binary)
 #DCDfreq Z-DCDfreq
 
 #standard output (section 3.2.3)
 #outputenergies Z-outputenergies       #number of timesteps between energy output
 #outputTiming Z-outputTiming           #number of timesteps between timing output
 
 #timestep parameters (section 5.3.1)
 firsttimestep           0              #frame number where the simulation starts
 #timestep Z-TIMESTEP
 stepspercycle           20             #how often the interacting particle lists are updated
 
 #space partitioning (section 5.3.2)
 cutoff                  12             #non-bonded cutoff
 switching               on             #smoothing function for ES and VDW
 switchdist              10             #distance at which the smoothing function is applied
 pairlistdist            16             #distance >= switchdist for atom pairs to be included in the pairlist
 margin                  0              #see section 5.3.2
 
 #basic dynamics (section 5.3.3)
 exclude                 scaled1-4      #which bonded atom pairs are excluded from non-bonded calculations
 #temperature Z-TEMPERATURE             #INITIAL temperature of the simulation note delete on restart
 1-4scaling              1.0            #1.0 for Charmm, 0.833333 for Amber
 #rigidbonds Z-RIGIDBONDS               #controls how shake is used (on or off)
 rigidTolerance          0.00001        #allowable bond length error for shake
 
 #PME parameters (section 5.3.5)
 PME                     yes            #turns PME on or off (yes=on no=off)
 pmeGridSpacing          1.0            # automatically assigns PME box sizes
 #constraints (section 6.1)
 constraints             on             #on or off
 #consref Z-CONSREF                     #pdb file with restraint reference positions
 #conskfile Z-CONSKFILE                 #pdb file with force constant values
 conskcol                B              #use beta column in pdb file 
 
 #temperature control and equilibration (section 6.3)
 langevin                on             #turns langevin dynamics on or off
 langevinTemp            310            #temp to which langevin dynamics will be adjusted
 langevinDamping         1              #damping coefficient for langevin dynamics
 
 #periodic boundry conditions (section 6.4.3)
 cellbasisvector1 $boxsize_x 0 0        #defines the first periodic boundary
 cellbasisvector2 0 $boxsize_y 0        #defines the second periodic boundary
 cellbasisvector3 0 0 $boxsize_z        #defines the third periodic boundary
 cellorigin $centerofbox                #defines the xyz location of the center of the box
 
 #extendedSystem Z-EXTENDEDSYSTEM       #defines file which contains the PBC info from previous runs
 wrapwater               on             #wraps the waters to one box.
 wrapall                 on             #wraps every contiguous cluster of bonded atoms
 wrapNearest             off            #wraps coordinates to the nearest image to the origin
 
 #pressure control (section 6.5)
 langevinPiston          on             #turns on constant pressure
 langevinPistonTarget    1.01325        #target pressure
 langevinPistonPeriod    200            #period over which the pressure is averaged in fs
 langevinPistonDecay     100            #damping time scale in fs
 langevinPistonTemp      310            #should be equal to langevin temp
 
 #equilibration
 #run Z-NSTEPS
 #minimize Z-NSTEPS

To increase parallelism for large number of processors, especially on Blue Gene, use

 twoAwayX   yes    # doubles the number of patches (divides the box in the x direction)
 twoAwayY   yes    # doubles the number of patches (divides the box in the y direction)
 twoAwayZ   yes    # doubles the number of patches (divides the box in the z direction)

==Sample minimization parameters==
Replace the following parameters in the generic namd input file above to perform a minimization.
The parameters which are not mention can remain commented out with the # before them.
We are doing 1000 steps of minimization at 310K and using shake on the water hydrogens only.

 outputname        01mi                                 
 coordinates       complex.solvated.pdb
 conskfile         restraint01.pdb
 structure         complex.solvated.psf
 temperature       310
 consref           reference.solvated.pdb
 langevinTemp      310                          
 minimize          1000                                  
 DCDfreq           1000
 outputenergies    1000
 outputTiming      1000
 rigidbonds        water

==Sample MD paramters==
This is a 500ps simulation with a timestep of 1fs. 03mi indicates the last namd run we are getting the input coordinates and velocities from. The xsc file contains the velocities. We are using shake on all the hydrogen atoms. Since we are using shake on all hydrogens, we could increase the timestep to 2fs to make this a 1ns simulation.
 
 outputname       04md
 coordinates      03mi.coor
 extendedSystem   03mi.xsc
 conskfile        complex.restraint04.pdb
 structure        complex.new.solvated.psf
 temperature      310
 consref          complex.new.solvated.pdb
 langevinTemp     310
 run              500000
 timestep         1
 DCDfreq          1000
 outputenergies   1000
 outputTiming     1000
 rigidbonds       all