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.ujep.cz>
To: "AMBER Mailing List" <amber.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.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.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 |
>>
>> 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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Received on Thu Nov 05 2009 - 10:30:04 PST
