I'd guess that all else being equal (e.g. force field, choice of
ensemble, thermostat type, MHE protocol, etc.) you won't get exactly
the same trajectory due to specific implementation details, but the
system will explore a potentially different but equally valid subset
of the phase space. So you'll likely be able to reproduce at least
macroscopic properties and structural change.
But yes, why not just use NAMD if you are trying to reproduce results
generated by NAMD?
--Tom
2010/5/24 Robert Elder <rmelder.gmail.com>:
> Catherine:
>
> My experience has been that sander and PMEMD yield essentially the same
> results as NAMD. I haven't directly compared trajectories from each program,
> but DNA helical parameters that I calculate are the same, within the limits
> of sampling. AMBER and NAMD use the same integration algorithms, I believe.
> (Correct me if I'm wrong!)
>
> Why not just use NAMD, though?
>
> Cheers,
> Robert Elder
> PhD Candidate -- University of Colorado-Boulder
>
> 2010/5/24 Catein Catherine <askamber23.hotmail.com>
>
>>
>> Dear Sir/Madam,
>>
>>
>>
>> Did any one compared the MD trajectory or binding energy results obtained
>> by NAMD or AMBER's sander or pnemed? I am trying to reproduce the results
>> of NAMD reported in literature, should I use sander or pnemed? I wonder if
>> similar aligorithems are used in NAMD and Sander/Pnemed?
>>
>>
>>
>> Best regards and many thanks for your advices,
>>
>> Catherine.
>>
>>
>>
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Received on Mon May 24 2010 - 14:00:03 PDT
