Yes, pmemd fully supports belly, but with the old mask syntax. Restraints
are generally a better choice though, for either sander or pmemd, due to the
nature of belly vs. restraints.
Regards - Bob Duke
----- Original Message -----
From: "Marek Maly" <marek.maly.ujep.cz>
To: "AMBER Mailing List" <amber.ambermd.org>
Sent: Thursday, November 05, 2009 8:36 AM
Subject: Re: [AMBER] pmemd vs sander.MPI
Hi Ross,
just the short question to this topic.
Is it after the proper syntax conversion (as you described below) possible
to use PMEMD also in case when part of simulated system
is totally froze using ibelly/bellymask approach ?
Thanks in advance for your info !
Best,
Marek
Dne Wed, 04 Nov 2009 19:33:23 +0100 Ross Walker <ross.rosswalker.co.uk>
napsal/-a:
> Hi Taufi,
>
>> I am using sander.MPI to run a dynamics simulation with a restraint
>> mask
>>
>> Molecular Dynamics for 2ns - only Surface atoms are fixed
>>
>> can i run the above with pmemd by changing the last two lines
>> Molecular Dynamics for 2ns - only Surface atoms are fixed
>
> Yes. PMEMD just needs the old restraint syntax. There is a tool called
> ambmask in $AMBERHOME/exe/ which will convert an AMBER mask into the old
> group format for you.
>
>> Also, i do remember talking with Dr. Walker about pmemd being faster
>> and
>> just as accurate as sander.MPI, is that also true when using 32 or 64
>> processors, or is it especially true when using large number of
>> processors?
>
> It will be a LOT faster. If you are running simulations within PMEMD's
> feature set you should probably always use it since it will be faster
> even
> on 1 processor. On 32+ it will make a big difference. You should be
> seeing
> performance equivalent to the following (this was run with pmemd)
>
> http://teragrid.org/userinfo/aus/amber_benchmark.php
>
> All the best
> Ross
>
>
> /\
> \/
> |\oss Walker
>
> | Assistant Research Professor |
> | San Diego Supercomputer Center |
> | Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
> | http://www.rosswalker.co.uk | PGP Key available on request |
>
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Received on Thu Nov 05 2009 - 06:00:04 PST
