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

From: Monika Madhavi (monikamadhavi_at_gmail.com)
Date: Thu Nov 02 2017 - 17:28:24 CDT

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.html, 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>
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>
> 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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