Re: RMSD of backbone changes rapidly at the beginning of production run

From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Thu Nov 02 2017 - 17:59:45 CDT

RMSD is always relative to a reference. Your reference is frame 0 of your simulation. The RMSD of frame 0 vs itself is per definition 0. Frame 1 relative to frame 0 is probably pretty small too, since there hasn't been much time to deviate away from the initial state. Each frame will deviate relative to your reference until they all look sort of samey, since your protein isn't (hopefully) going to unfold, and will explore conformations around its folded basin. In short, the behavior you describe seems perfectly normal to me. What was the asymptotic value? Something close to the resolution of the crystal structure probably?

-Josh

On 11/02/2017 04:34 PM, Monika Madhavi wrote:
Hi Peter,

Here are my configuration parameters

#############################################################
## ADJUSTABLE PARAMETERS ##
#############################################################

structure wat_collagen.psf
coordinates wat_collagen.pdb

set temperature 280
set outputname col_run28010

#Continuing a job from the restart files
set inputname eq03_res20
binCoordinates $inputname.restart.coor
binVelocities $inputname.restart.vel
extendedSystem $inputname.restart.xsc

firsttimestep 0

#############################################################
## SIMULATION PARAMETERS ##
#############################################################

# Input
paraTypeCharmm on
parameters ../setup/par_all27_prot_lipid_HYP.inp
#temperature $temperature

# Force-Field Parameters
exclude scaled1-4
1-4scaling 1.0
cutoff 10.0
switching on
switchdist 8.0
pairlistdist 12.0
waterModel tip4

# Integrator Parameters
timestep 1.0 ;# 1fs/step
rigidBonds all ;# needed for 2fs steps
nonbondedFreq 1
fullElectFrequency 2
stepspercycle 10

# Constant Temperature Control
langevin on ;# do langevin dynamics
langevinDamping 1 ;# damping coefficient (gamma) of 1/ps
langevinTemp $temperature
langevinHydrogen off ;# don't couple bath to hydrogens

# Periodic Boundary Conditions
cellBasisVector1 62.00 0.0 0.0
cellBasisVector2 0.0 62.00 0.0
cellBasisVector3 0.0 0.0 120.00
cellOrigin 0.251 0.107 0.138

wrapAll on

# PME (for full-system periodic electrostatics)
PME yes
PMEGridSpacing 1.0

# Constant Pressure Control (variable volume)
useGroupPressure yes ;# needed for rigidBonds
useFlexibleCell no
useConstantArea no

langevinPiston on
langevinPistonTarget 10.1325 ;# in bar -> 10 atm
langevinPistonPeriod 100.0
langevinPistonDecay 50.0
langevinPistonTemp $temperature

#set contrains on CA atoms
constraints on
consRef restrain_ca20.pdb
consKFile restrain_ca20.pdb
consKCol B

# Output
outputName $outputname

restartfreq 1 ;# 1 steps = every 0.001 ps
dcdfreq 1
xstFreq 1
outputEnergies 1
outputPressure 1

#############################################################
## EXECUTION SCRIPT ##
#############################################################

run 10000000

I calculated rmsd using the example script provided in the link http://www.ks.uiuc.edu/Research/vmd/vmd-1.7.1/ug/node185.htmlda8c%7Ca0f29d7e28cd4f5484427885aee7c080%7C0%7C0%7C636452588596896194&sdata=P8JowEJt%2BJ0hC7fqLpGdJ4vX%2F%2BEvCe%2BNffpTgAER5Xo%3D&reserved=0>, changing the atomselection to backbone atoms.

# Prints the RMSD of the protein atoms between each timestep
        # and the first timestep for the given molecule id (default: top)
        proc print_rmsd_through_time {{mol top}} {
                # use frame 0 for the reference
                set reference [atomselect $mol "backbone and protein" frame 0]
                # the frame being compared
                set compare [atomselect $mol "backbone and protein"]

                set num_steps [molinfo $mol get numframes]
                for {set frame 0} {$frame < $num_steps} {incr frame} {
                        # get the correct frame
                        $compare frame $frame

                        # compute the transformation
                        set trans_mat [measure fit $compare $reference]
                        # do the alignment
                        $compare move $trans_mat
                        # compute the RMSD
                        set rmsd [measure rmsd $compare $reference]
                        # print the RMSD
                        puts "RMSD of $frame is $rmsd"
                }
        }

Thank you.

Best regards,

Monika

On Fri, Nov 3, 2017 at 12:02 AM, Peter Freddolino <petefred_at_umich.edu<mailto:petefred_at_umich.edu>> wrote:
You would need to provide more information, such as your config files and how you measured the rmsd, in order to get a useful response...
Best,
Peter

On Thu, Nov 2, 2017 at 5:52 AM, Monika Madhavi <monikamadhavi_at_gmail.com<mailto:monikamadhavi_at_gmail.com>> wrote:
Dear all,

I did a MD simulation of an amino acid chain in water having strong constrains applied to backbone atoms. Prior to the production run I equillibriated the system in constant temperature and pressure and used the extended system files to start the production run. When I calculated the RMSD of the backbone, I expected to see a minimal fluctuation in RMSD but I see a sudden increase in RMSD just after the simulation is started and then it follows a damped oscillatory behavior before it reaches an asymptotic value. I wonder what could be the reason for that kind of a behaviour, is it due to something wrong with my configuration parameters?

Thank you.
Best regards,
Monika 

--
W.A.Monika Madhavi
Lecturer (Probation),
Department of Physics,
University of Colombo.
--
W.A.Monika Madhavi
Lecturer (Probation),
Department of Physics,
University of Colombo.

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