AMBER Archive (2009)

Subject: Re: [AMBER] PMEMD vs GROMACS?

From: Vlad Cojocaru (Vlad.Cojocaru_at_eml-r.villa-bosch.de)
Date: Tue Feb 24 2009 - 02:24:16 CST

Hi Sasha,

Well .. Its a good question what you are asking ... There are however
other MD software which are widely used such as NAMD, CHARMM and so on ...
GROMACS 4.0 seems to be fast indeed. However, on our small cluster here
I have NAMD and PMEMD scaling up to 64 cores while GROMACS scales only
until 16 or 32 depending on the system ..

But the main difference between these programs is the force fields you
can use with them (and make sure not to mix the names of the programs
with the names of the force fields, that's why I use upper case for
programs, lower case for force field names). AMBER is designed to work
with the force fields based on Cornell et al. 94 (amber force fields),
GROMACS works with opls and gromos force fields, NAMD works mainly with
charmm. In NAMD you can also use the amber force fields if you follow
strictly the recommendations. In GROMACS you cannot use neither charmm,
nor amber force fields unless you implement it yourself.

There are also slight differences in the options provided by these
programs. One typical issue is the pressure coupling scheme for NPT
simulations. GROMACS and NAMD provide more options here while AMBER only
provides Berendsen's coupling algorithm. So, if you run membrane
simulations, AMBER is still limited. In return, AMBER works with the
glycam force filed for sugars. So, if you have a glycosylated protein,
then probably you'd like to use the glycam force field to treat the
sugar(s).

At the end, it comes down to which force field you'd like to use. And
this is dependent on the problem you are investigating. If you have
membranes, even if you'll use the amber force fields (e.g gaff), you
might want to use the NAMD program for the runs as it allows more
sophisticated pressure coupling algorithms. If you have only soluble
proteins, it probably depends very much what specific issue you are
investigated. All these force fields seem do well on some protein issues
and not well on others. If you have nucleic acids, the amber force
fields are probably the most widely used, although the charmm force
fields have also been successfully applied.

Only after deciding the force field you want to use, it comes down to
the program you want to use depending on the architecture you have.
NAMD is well known to do very well on scaling up to thousands of cores
on big computers such as Blue Genes. GROMACS is still lagging behind in
terms of scaling although its very fast. With PMEMD, I do not have
experience on big machines, but PMEMD is faster comparing to NAMD on up
to 64 cores on opteron clusters. Unfortunately, PMEMD has still limited
functionality. For methods such as SMD, Umbrella Sampling, Targeted MD
you still need to use SANDER, and this is much slower and scales much
worse. That's why I always use NAMD with the amber force fields if I
need to do such calculations.

After this, you need to read literature on your specific topic to see
what to use and how ...

Cheers
vlad

Sasha Buzko wrote:
> Hi all,
> I wonder if anyone has had any comparative experience with pmemd and
> gromacs. The latter seems to be faster, but what about the simulation
> outcomes? Are the results identical/similar and if there are
> differences, how significant?
>
> And if the results are comparable, a more general question: why
> doesn't everyone just switch to using gromacs? Are there other issues
> that come into play?
>
> Thanks for any insight.
>
> Sasha
>
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
> 

-- 
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Dr. Vlad Cojocaru

EML Research gGmbH
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Tel: ++49-6221-533202
Fax: ++49-6221-533298

e-mail:Vlad.Cojocaru[at]eml-r.villa-bosch.de

http://projects.villa-bosch.de/mcm/people/cojocaru/

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