AMBER Archive (2008)

Subject: Re: AMBER: Sander instead of PMEMD

From: Cristina Sisu (csds2_at_cam.ac.uk)
Date: Fri May 30 2008 - 10:22:10 CDT

Thanks for the hint! I'll try it right away.

Cheers,
Cristina

Florian Haberl wrote:
> Hi,
>
> On Friday, 30. May 2008 16:32, Cristina Sisu wrote:
>
>> Thanks Bob,
>>
>> Then I think I will give it a try with sander. Fingers crossed!
>> But are you sure that pmemd does not support mm_pbsa? Because according
>> to the mmpbsa tutorial, it should work
>> http://amber.scripps.edu/tutorials/advanced/tutorial3/section2.htm.
>>
>>
>
> the mm pbsa analysis is a post analysis, so you have to seperate the snapshots
> and than recalculate it with sander. If the simulation is done with sander or
> pmemd doesn`t matter, the only difference is than pmemd is faster ;)
>
> A small hint before starting mm pbsa analysis: It is faster to transfer the
> trajectory to your wanted snapshot frequency (normally every 25 or 50ps),
> before starting mm pbsa analysis.
>
> greetings,
>
> Florian
>
>
>
>> Cristina
>>
>> Robert Duke wrote:
>>
>>> The primary advantage pmemd offers is purely speed; there are a few
>>> minor convenience tweaks here and there, but it is mostly supposed to
>>> do a subset of sander functionality, not the other way around. So
>>> there should never be a problem moving back to sander from pmemd, as a
>>> general rule. Also note that pmemd does not support energy
>>> decomposition through the idecomp switch, and therefore does not
>>> support mm_pbsa anyway.
>>> Regards - Bob Duke
>>>
>>> ----- Original Message ----- From: "Cristina Sisu" <csds2_at_cam.ac.uk>
>>> To: <amber_at_scripps.edu>
>>> Sent: Friday, May 30, 2008 9:47 AM
>>> Subject: AMBER: Sander instead of PMEMD
>>>
>>>
>>>> Dear Ambers,
>>>>
>>>> I have a problem running PMEMD on our cluster. As far as I understand it
>>>> does not seem to be a program problem but rather the way that our
>>>> cluster is build (on module, environments, etc.). I want to do some
>>>> MMPBSA calculations on a protein-peptide ligand complex. Can I use for
>>>> the production run, Sander instead of the PMEMD? With the periodic
>>>> boundary condition parameter switched on, and using the same input (.in)
>>>> file as for PMEMD?
>>>> Would the trajectory obtained in this way be suitable for extracting
>>>> snapshots necessary for mmpbsa ?
>>>>
>>>> Thanks,
>>>> Cristina
>>>>

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