AMBER Archive (2006)

Subject: Re: AMBER: AMBER 8 VS AMBER 7

From: Carlos Simmerling (carlos_at_ilion.bio.sunysb.edu)
Date: Thu Mar 02 2006 - 15:04:09 CST

I would add to this that you changed the temperature
coupling method between the two runs, and that probably
has a larger effect than the different Amber version. It's always
hard to track down a problem when you change multiple things
at once. Try to repeat your Amber7 approach with Amber 8
before changing the simulation methods.

David A. Case wrote:
> On Thu, Mar 02, 2006, venditti2_at_unisi.it wrote:
>
>
>> I carried out two simulations on the same RNA molecule using both AMBER 8
>> and AMBER 7.
>>
>
>
>> Surprisengly the minimized structures look very diffent
>>
>
> This is surprising, since a few thousand steps of energy minimization rarely
> changes the structure very much. Presumably(?) there could be no differences
> in the restrained minimization [unless you in fact had different starting
> structures....]. Even an unrestrained minimization for such a short time
> should not do much -- *unless* you have some very bad forces and energies
> in the starting structures.
>
>
>> and the
>> unrestrined MD trajectories show a very different behaviour:
>>
>
> This is to be expected, given what you said: if the minimized structures
> (which are what you used to start the MD) are very different, then the
> MD simulations themselves are likely to be different.
>
> You don't give much information, but I would look at the minimization step
> to see if you can figure out what is going on there.
>
> [All of this should have nothing to do with Amber 7 vs. Amber 8. To test
> this, run a short MD or minimization (just a few steps), set ntpr=1, and
> compare the results with both programs.]
>
> ...dac
>
>
>> Keep RNA fixed with weak restraints
>> 10.0
>> RES 1 24
>> END
>> END
>>
>
> Just a comment on the above: restraints with a force constant of 10 are in
> fact very strong restraints; a "weak" restraint would be something like 100
> times smaller than that.
>
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