Re: [AMBER] Different trajectories with different RMSD with changing the parameters of gamma_ln, taup, timesteps and extend of density equilibration

From: Rajesh Raju <>
Date: Fri, 08 Jul 2011 17:46:56 -0500

Dear Prof. Cheatham,

Thank you very much for ur reply. Now I got more idea about MD.

Also one more doubt, how can I make sure that the system reached
equilibration? My systems contains 437 res and 14500 water molecules.
When I checked the density of the system its close to 0.99 or 0.98
always.. So I thought it equilibrated very well..If the system doesnt
reach the equlibration stage, how can I know that....?

  Is 2ns equilibration is sufficient..?

Now I m going to do a number of simulations taking into account ur

I will consider these changes as u mentioned.. taup = 0.2 for
equlibration, cut=9A and forcefield changes....

" [Instabilities could also result from the force field; I would
> ff99SB + parmbsc0 for the protein-DNA]. "

can use SO Can I use FF10 forcefield? I have seen from Amber 11 manual
that FF10 includes both of these...

Thank you very much for ur reply...


On Fri, 8 Jul 2011 15:49:34 -0600 (Mountain Daylight Time)
  Thomas Cheatham III <> wrote:
> Re:
> Note that if people do not reply in a timely manner, please do not
> repost older messages. Try re-phrasing / condensing and/or make it
> clear that you are asking again since you did not get sufficient
> previously.
>> I am working on DNA-protein interactions. I have followed the
>> following steps:
> ...
>> I have performed 9 (A-I) different simulations with different
>> temperature coupling parameter (gamma_ln ) and pressure couling
> ...
>> I calculated the RMSD deviations withrest to the first frame (BLACK
>> lines in the RMSD plots) in the production stage and also with
>> to the minimized structure after minimzation step2 (RED lines).. I
>> have attached the RMSD plots. The RMSD plots shows a large variation
>> upon changing the simulation parameters..?
> ...
>> If these trajectories differ by changing the simulations parameters,
>> how we can trust these results?
> MD simulations are chaotic and small changes in parameters or
> conditions (and/or parallelism) will lead to different results. As
> pointed out by Professor Roitberg, a key question is whether the
> differences are expected and/or statistically significant.
> Before assuming that the differences observed are real, convince
> that they are statistically significant. Roitberg suggested that
> cannot easily compare results from different runtime parameters
> gamma_ln); you replied that perhaps that meant you should re-run all
> simulations (to which no one replied).
> Since you have set ig=-1, re-running should lead to different
> (noting that you may want to set ig=-1 in the heat1 phase).
> However, you
> need not re-run all of them. Pick one set of conditions (gamma_ln,
> dt) and run these simulations multiple times. What you likely will
> observe is similar differences to what you saw previously under
> conditions, i.e. that the system has not converged and the results
> considerably from simulation to simulation (although I could be
> here). Another good way to get different initial conditions is to
>use a
> different ion distribution (you can use randomizeions in ptraj).
>> Is there any 'best parameters for gamma_ln and taup.
> The less often you perturb the temperature, the better, however I
> not expect significant differences in the results for simulations
> gamma_ln = 1 or 2 or 3. For equilibration, I set taup smaller (0.2
> 1.0) to get the pressure correct quickly, and then during production
> either run constant volume or set taup larger (5.0, 10.0) for less
> perturbation.
>> Is there any problems in the MD protocol which I followed?
> The protocol is (mostly) fine; likely the observed differences are
> statistically significant.
>> What is the reason for the odd behaviour in the RMSD plots and what
>> should I do to get a stable MD trajectory?
> A subtlety relates to the restraints on the protein+DNA with
> pressure since the positions of the molecules are scaled shifting
> relative positions of the molecules as the simulation runs. If the
> size changes significantly (it shrinks by default with standard LEaP
> solvateOct/solvateBox), this can lead to the molecules getting
> together despite the restraints. To get around this, the molecules
> to be merged into a single molecule which requires hacking the
> If this molecule shifting is leading to instability (i.e. the
> distortion you are seeing), you can try turning off the restraints
>or use
> only positionally independent restraints (like h-bonds) on the
> structures. Or only restrain one of the molecules (i.e. protein).
> Now, looking at the RMSd plots, we must wonder if differences of 1-3
> Angstrom are significant? Atoms have net thermal motion so we
>expect some
> RMSd; also, the more atoms, the larger the RMSd will be. To check
> out you need to look at average structures and compare them from the
> different simulations. I suggest creating average structures from
> and comparing them. You may also consider looking at 2D-RMS plots
> across an individual trajectory or all pooled together to show
> similarities).
>Finally, as pointed out by Dan Roe, 4 ns is clearly not sufficient to
> relax the protein, DNA, solvent and ion environment. This may
> longer...
> Note also:
>> Heating Stage 1
>> &cntrl
>> cut = 12.0,
>> /
> The cutoff is rather large for an explicit water simulation with
> would suggest 8.0 or 9.0 angstroms, but first convince yourself that
> small differences in the results between modest changes in time step
> Langevin coupling are real.
> [Instabilities could also result from the force field; I would
> ff99SB + parmbsc0 for the protein-DNA].
> --tec3
> _______________________________________________
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Received on Fri Jul 08 2011 - 16:00:03 PDT
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