AMBER Archive (2008)

Subject: Re: AMBER: restarting molecular dynamics

From: Adrian Roitberg (roitberg_at_qtp.ufl.edu)
Date: Wed May 28 2008 - 10:48:45 CDT

Germain,
ok, I get it now.

So, you are correct, the difference between your one-step run and the
dashed run is basically precision in the restart file.

I would be curious as to how long do they take to diverge from each
other. This is of course not a trivial quantity to gauge, but I would
not be surprised if they are different after 1 ps or so.

Cheers
a.

Germain Vallverdu wrote:
> Dear Adrian
>
>>
>> It is VERy unclear to me what you mean by "a simulation of about 10
>> ps step by step with a restart every 5fs". Do you mean that you will
>> stop every 5 fs, and restart again for another 5 fs and so on until
>> you reach 10 ps ? Why would you do that ?
>>
> Yes I would like exactly do that. I would like to do a simulation with
> variable charges. Then every 5fs I stop the run, compute (or not) new
> charges and restart the run again.
>> I also do not understand what you mean by "compare the one step
>> run with the dashed run".
> I have done one run with a length of 10 ps and one "dashed" run ( where
> I stop and restart every 5 fs). For these tow runs I plot the
> trajectories of a coordinate of interest and look for differences
> between them. I see that the curves are similar during the first ps and
> then are different. Nevertheless the mean and the standard deviations
> are similar.
>>
>> Regardless of that, you are basically right about what sander does
>> when it restarts:
>>
>> "> I suppose that :
>> > - when sander start it computes the PME grids
>> > - if I use algorithm control of the temperature like Langevin or
>> > Andersen perhaps there is a repeat of the random number chain
>> because of
>> > the seed is the same for every run.
>> > - the accuracy of the coordinate and velocities is better in the
>> program
>> > than in restrt files. Then this might lead to difference between
>> > trajectories."
>>
>> but you are using ntt=1 (Berendsen thermostat) so thgere are no random
>> number sequences for the temperature control.
> Yes that is exactly why I chose this one.
>> Indeed, the precision of the restart file is different than the
>> internal precision during calculations, and different from the
>> dynamics coordinates in the mdcrd files.
>>
> Then do you think this is the only origins of differences between the
> trajectories ?
>
> Best whiches
>
> Germain
>> So, please clarify what you want to do and we might be able to help you.
>>
>> Cheers
>>
>> adrian
>>
>>
>> Germain Vallverdu wrote:
>>> Hello Amber
>>>
>>> I would like to know exactly what append when I restart a molecular
>>> dynamics with sander.
>>>
>>> here is an example of my input file, I use AMBER 9 on a Linux system.
>>> This is a simulation of an organic molecule in a TIP3P water box.
>>>
>>> &cntrl
>>> nstlim=50000, dt=0.001,
>>> irest=1, ntx=5,
>>> ntpr=100, ntwr=100, ntwx=0,
>>> tempi=300.0, temp0=300.0, ntt=1,
>>> ntb=2, pres0=1.0, ntp=1, taup=2.0,
>>> ntc=2, ntf=2,
>>> cut=10.0,
>>> /
>>>
>>> My problem is the following. I would like to do a simulation of about
>>> 10 ps step by step with a restart every 5fs. But if I compare the one
>>> step run with the dashed run, trajectory are not similar after few
>>> steps. Then I would like to know what exactly append when Sander starts.
>>>
>>> I suppose that :
>>> - when sander start it computes the PME grids
>>> - if I use algorithm control of the temperature like Langevin or
>>> Andersen perhaps there is a repeat of the random number chain because
>>> of the seed is the same for every run.
>>> - the accuracy of the coordinate and velocities is better in the
>>> program than in restrt files. Then this might lead to difference
>>> between trajectories.
>>>
>>> Nevertheless do you think that something like that is possible to do
>>> and does it exist other process at the beginning of sander ?
>>>
>>> Best wishes
>>>
>>> Germain
>>>
>>
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-- 
                            Dr. Adrian E. Roitberg
                              Associate Professor
                             Quantum Theory Project
                            Department of Chemistry

                  Senior Editor. Journal of Physical Chemistry
                           American Chemical Society

University of Florida                         PHONE 352 392-6972
P.O. Box 118435                               FAX   352 392-8722
Gainesville, FL 32611-8435                    Email adrian_at_qtp.ufl.edu
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