AMBER Archive (2008)

Subject: Re: AMBER: Sander instead of PMEMD

From: Robert Duke (rduke_at_email.unc.edu)
Date: Fri May 30 2008 - 09:50:36 CDT

Hi Cristina -
Well, what pmemd does not support is the idecomp capability for energy
decomposition. It looks like there are other things that can be done with
mm-pbsa without using this, so I guess if that is what you are doing, you
are okay. I have not had occasion to use this stuff myself, and had not
gone through this tutorial. If indeed this tutorial represents all the
capability you need, and there is not an mdin down the line with an idecomp
entry, you all may want to figure out why your cluster is not running pmemd,
especially if it is infiniband. If you have a decent interconnect, the
better performance does make life much more pleasant (and if you can get
sander to work on the cluster, you should be able to get pmemd to work,
aside from my "weak" (ie., no) support for things like gfortran).
Regards - Bob

----- Original Message -----
From: "Cristina Sisu" <csds2_at_cam.ac.uk>
To: <amber_at_scripps.edu>
Sent: Friday, May 30, 2008 10:32 AM
Subject: Re: AMBER: Sander instead of PMEMD

> 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.
>
> 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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