I am trying to run a production run of 1 nano second in NAMD. Everything is OK till first few hundred Picoseconds. But after that my protein runs out of water-box. please have a look at frames of trajectory that shows how it escapes the water box. It looks very awful while visualizing the trajectory. It is understandable if a little portion of protein pokes out of box and we can assume that it might interact with water molecules in neighboring periodic image since we are using periodic boundary conditions. But complete escape of protein out of solvent box really concerns me. I am also pasting the content of my production run configuration file here.
My question is that is there any way or method by which I can limit my protein to stay inside the water box till simulation finishes. I also quite don't understand why my system is behaving this way because the protein remains well inside the box during equilibration stage. Your suggestion for my problems are highly appreciable!
Content of configuration file:
##############################################
#### input topology and initial structure ####
##############################################
structure 0301_AVTPTVATR.psf
coordinates 0301_AVTPTVATR_equil010.coor
###########################
#### force field block ####
###########################
paratypecharmm on
parameters forcefield
exclude scaled1-4
1-4scaling 1.0
dielectric 1.0
##############################################
#### dealing with long-range interactions ####
##############################################
switching on
switchdist 10.0
cutoff 12.0
pairlistdist 14
margin 2.5
stepspercycle 20
rigidBonds all
#######################################################
#### this block specifies the Ewald electrostatics ####
#######################################################
PME yes
PMEGridSpacing 1.0
PMEGridSizeX 90
PMEGridSizeY 86
PMEGridSizeZ 100
####################################################################
#### this block specifies the parameters for integrator and MTS ####
####################################################################
timestep 2.0
fullElectFrequency 2
####################################################################
######## this block determines the output ##########################
####################################################################
outputenergies 100
outputtiming 100
binaryoutput no
outputname 0301_AVTPTVATR_quench010
restartname 0301_AVTPTVATR_restart_quench010
restartfreq 500
binaryrestart no
DCDfile 0301_AVTPTVATR_quench010.dcd
dcdfreq 500
####################################################################
####################### MD protocol block ##########################
####################################################################
seed 3010
numsteps 500000
temperature 300
####################################################################
######## this block defines periodic boundary conditions ###########
####################################################################
cellBasisVector1 87.72 0.0 0.0
cellBasisVector2 0.0 83.14 0.0
cellBasisVector3 0.0 0.0 97.76
cellOrigin 3.60659217834 -1.9387652874 4.90524196625
wrapWater on
You haven't set up imaging correctly. With "wrapWater on," you're only reconstructing water molecules in the unit cell. You need "wrapAll on" to apply imaging to the remaining elements of the system.
You haven't set up imaging correctly. With "wrapWater on," you're only reconstructing water molecules in the unit cell. You need "wrapAll on" to apply imaging to the remaining elements of the system.
Most of those settings are highly specific to that particular system (looks like it's from a tutorial) and the output frequency is way too high for normal usage. The solution is very simple; large-scale changes to the input file are not needed, just the single keyword I said before.
PRITAM KUMAR PANDA: First of all, let me first correct you that it is configuration file that you use for running simulation, we use topology file for generating pdb+psf pair. Anyways... I understood what you meant to say. Second, you have some serious issues in your configuration file, say for instance, you have used timestep of 3 FS and you intend to run the simulation for 1000 steps. This will give you simulation time of 3*1000=3000, which is not equal to 1 NS. Please go through the simulation time section in NAMD userguide to know how many steps will be required for running simulation of 1NS. Using higher values for timestep in short simulations (say for example 1NS) will eventually lead to poor sampling. You should be very cautious while setting these parameters in configuration file because only running the simulation do not really matter; what matters is running CORRECT simulation. Third, it seems that you have provided me configuration for doing EQUILIBRATION simulation, in contrary I wish to perform PRODUCTION simulation. I have mentioned that I have already equilibrated my system. SO.... that wont help me either, but I really appreciate and thank you for your kind support
SO far your question is concerned, Yes... it is possible to run simulation for 5ns in laptop using configuration you provided. YOu shall need to make modifications in following sections
1. YOur values for cellBasisVector in Periodic Boundary Conditions section are exactly same as PMEGridSize. you need to check this out.
2. You need to select proper values for timestep and numstep . you can use 2 Fs for timestep and run the simulation for 2500000 steps that will give simulation time of 5000000 (=5NS)
3. Manage number of processors to use in simulation properly while you run the simulation. i5 processor have 4 cores, so at max, you can use +p4 option while running program.
4. Give rest to your computer at proper interval (if you are using +p4), set proper hibernation time in your laptop if you need to run continuous 5 NS simulation. Laptops are not designed to do high computation intensive heavy simulation work. You can end up burning your processor cooling fan. Believe me I have burnt one and my PhD guide was not so happy about it!!! I would advise you to split and run 5 NS simulation in two 2.5 NS simulations (or five 1 NS simulations). Hope this helps
@ PRITAM KUMAR PANDA
Try out this tutorial
http://faculty.uml.edu/vbarsegov/teaching/bioinformatics/lectures/MDSimulationsModified.pdf
- Badges
- Science topic
- Similar topics
- Chemistry
- Theoretical Chemistry
- Computational Chemistry
- Molecular Dynamics