AMBER Archive (2009)

Subject: Re: [AMBER] pmemd vs sander.MPI

From: Marek Maly (marek.maly_at_ujep.cz)
Date: Thu Nov 05 2009 - 12:34:31 CST

OK,
to be frank I am even not sure if for example this selection of residui
:LGM,WAT is in a NEW or OLD selection syntax :))

I just know that I am using this syntax and I don't know about the second
syntax possibility ...

So maybe Ross could put some light here to understand better what is what
and how
to convert easily this two syntaxes.

But anyway thanks again for your comments and thanks in advance to
anybody, who
can comment more in detail the "new/old syntax" topic.

   Best,

     Marek

Dne Thu, 05 Nov 2009 19:06:24 +0100 Robert Duke <rduke_at_email.unc.edu>
napsal/-a:

> Sorry, I don't ever use the "new syntax"; Ross or somebody who does
> routinely can probably more reliably do this for you... - Regards - Bob
> ----- Original Message ----- From: "Marek Maly" <marek.maly_at_ujep.cz>
> To: "AMBER Mailing List" <amber_at_ambermd.org>
> Sent: Thursday, November 05, 2009 1:03 PM
> Subject: Re: [AMBER] pmemd vs sander.MPI
>
>
> Hi Bob,
> thanks a lot for this good news !
>
> Could you please ( if it is not so time consuming ) rewrite
> this two lines using so called "old mask syntax" ?
> (Is this "old mask syntax" described in detail somewhere ?)
>
> ---------------------------
>
> ibelly = 1,
> bellymask=':LGM,WAT',
>
> --------------------------
>
> I assume, that probably only this part: ':LGM,WAT' should be changed
> somehow.
>
> Ross pointed out that the conversion could be done with AMBMASK tool, but
> after
> short look in Amber10 manual it is not clear to me, how to use it for our
> simple purpose.
> If I understood well AMBMASK is flexible tool to dump some selected
> atoms,
> residui to
> some output file and not just a simple tool for conversion of the mask
> syntax from
> actual to old, but probably it could be used this way as Ross mentioned
> it
> in this connection,
> but would be better to see practical example, how to do this particular
> AMBMASK task.
>
>
> Thank you in advance for any additional comments !
>
> Best
>
> Marek
>
>
>
>
> Dne Thu, 05 Nov 2009 14:35:41 +0100 Robert Duke <rduke_at_email.unc.edu>
> napsal/-a:
>
>> 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_at_ujep.cz>
>> To: "AMBER Mailing List" <amber_at_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_at_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_at_rosswalker.co.uk |
>>> | http://www.rosswalker.co.uk | PGP Key available on request |
>>>
>>> Note: Electronic Mail is not secure, has no guarantee of delivery, may
>>> not
>>> be read every day, and should not be used for urgent or sensitive
>>> issues.
>>>
>>>
>>>
>>>
>>>
>>>
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>>>
>>
>>
>>
>
>
> 

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