From: Peter Freddolino (petefred_at_umich.edu)
Date: Thu Nov 02 2017 - 20:25:17 CDT
Hi Monika,
Can you also elaborate a little on how high the rmsd gets during this
"sudden increase" that you noted? As Joshua points out, if this is on the
order of a couple of angstroms, it is perfectly normal.
Also, a couple of issues that pop out:
-your output frequencies are very high, which means you're going to end up
with HUGE output files. Because MD values have high autocorrelations, there
is really no reason to keep every frame unless you have some edge case that
absolutely requires it.
-that rmsd script that you posted is VERY old -- from vmd 1.7.1! I would
recommend using the RMSD trajectory tool plugin instead.
Best,
Peter
On Thu, Nov 2, 2017 at 6:28 PM, Monika Madhavi <monikamadhavi_at_gmail.com>
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.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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