AMBER Archive (2008)

Subject: Re: AMBER: pmemd iwrap trouble

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Mon Aug 25 2008 - 11:35:53 CDT

Bob- a an aside to this, I'm having trouble with ptraj imaging pmemd
traj files. I never had this with sander, but with pmemd many of the
frames don't properly image a dimer. Do you know which ptraj image
syntax/options match that used in pmemd? I'm using this, which always
works for sander for an 830 residue protein (415 in each monomer). I
want the dimer to be reconstructed properly.

center :1-415 mass origin
image origin center familiar

but often the imaging isn't right- the rmsd for the dimer is a few A
larger than it should be, and then it hops back to normal values. you
can also see shifts in the dimer during the MD in VMD< then it hops
back again. I know it's an imaging issue- do you know how to fix it?
thanks
carlos

On Mon, Aug 25, 2008 at 11:45 AM, Robert Duke <rduke_at_email.unc.edu> wrote:
> Hi Lars,
> It should be perfectly compatible; I just checked over the code and iwrap is
> used regardless of box type for both restart and mdcrd. However, I do
> believe that if ioutfm = 1 (ie., binary restart file), it is true that
> wrapping does not occur. It is actually not needed in the case of a binary
> restart - overflow is not practically possible. We should probably document
> this "feature" or release a patch to change the behaviour (the problem is
> caused by the fact that writes of the binary restarts occur on the actual
> coordinates, whereas all wrapping is done on a temporary copy of the
> coordinates because you don't want to actually wrap the coordinates
> internally. This should not be affecting your trajectory, just the restart
> file. Since you see this with ioutfm 0, I suspect this is also an issue of
> the truncated octahedron not looking right in vmd, but am not at all
> certain. Seems I once heard Darden say something about this stuff (I think
> he wrote the trunc. oct. wrapping code). Tom? I'll look at all the
> relevant code in both pmemd and sander later in the week when I have my
> source machine up, talk to other key amber guys, and post something to the
> list as to what, if anything we intend to do about binary restarts not being
> wrapped.
> Best Regards - Bob
>
> ----- Original Message ----- From: "Lars Skjærven"
> <lars.skjarven_at_biomed.uib.no>
> To: <amber_at_scripps.edu>
> Sent: Monday, August 25, 2008 10:58 AM
> Subject: Re: AMBER: pmemd iwrap trouble
>
>
>> Hi again,
>> I did some more testing without any results.. It seems to me that
>> iwrap = 1 is not compatible with octahedral water box?
>> Lars
>>
>> On Mon, Aug 25, 2008 at 3:32 PM, Lars Skjærven
>> <lars.skjarven_at_biomed.uib.no> wrote:
>>>
>>> Hi Bob,
>>> Thanks for the quick reply. removing ioutfm=1 does not yield a
>>> different result. nor changing to sander. :-/
>>>
>>> getting rid of some of my input variables the input-file looks like this
>>> now:
>>>
>>> Wrap
>>> &cntrl
>>> imin= 0, irest= 1, ntx = 5,
>>> ntb = 1,
>>> cut = 10,
>>> ntc = 2, ntf = 2,
>>> ntt = 0,
>>> nstlim = 1, dt = 0.001,
>>> iwrap = 1, ioutfm=0
>>> /
>>>
>>> Am I sure it is not just an imaging problem?
>>>
>>> I think its not: In the multimer simulation (which gets a few subunits
>>> displaced during the run with iwrap=1) the rmsd jumps from 3Å to 80Å
>>> when doing rmsd analysis in ptraj. for the monomer simulation the rmsd
>>> does not yield an immediate jump, but continuing the simulation after
>>> iwrap=1 yields and increasing rmsd value after a few more ns. maybe
>>> implying that the protein has been translated and starts interacting
>>> with an image?
>>>
>>> I will continue working on this and let you know if I find anything
>>> else..
>>>
>>> Cheers,
>>> Lars
>>>
>>>
>>> On Mon, Aug 25, 2008 at 2:40 PM, Robert Duke <rduke_at_email.unc.edu> wrote:
>>>>
>>>> Hi Lars,
>>>> I am on vacation today, but will look at it tomorrow. There should not
>>>> be a
>>>> problem with wrapping in amber 10 pmemd; there was a bug in amber 9
>>>> pmemd
>>>> for which a patch was released. That said, I am not sure there is not
>>>> some
>>>> intricacy when binary trajectory files are in use, and I will have to
>>>> look.
>>>> It should not matter, as the restart file is the primary issue here, and
>>>> it
>>>> is not binary, but maybe there is some combination of inputs that screws
>>>> up
>>>> on wrapping. Are you sure it is not just an imaging problem? I have
>>>> grief
>>>> going back and forth between what pmemd or sander does and what ptraj
>>>> does
>>>> (but I am talking constant pressure here, and ptraj I think hits grief
>>>> with
>>>> the changing boxsize). Anyway, I will look into it, but you might try a
>>>> 1
>>>> step, no binary output run just for grins, or do a single step in sander
>>>> and
>>>> see if you get the same result (just gives me more info, in case
>>>> something
>>>> obvious does not jump out).
>>>> Thanks - Bob Duke
>>>>
>>>> ----- Original Message ----- From: "Lars Skjærven"
>>>> <lars.skjarven_at_biomed.uib.no>
>>>> To: <amber_at_scripps.edu>
>>>> Sent: Monday, August 25, 2008 6:25 AM
>>>> Subject: AMBER: pmemd iwrap trouble
>>>>
>>>>
>>>>> Dear Amber users,
>>>>>
>>>>> I've been running a MD-simulation for about 40ns and needed to wrap
>>>>> the water back into the primary box (due to water has swimed too far
>>>>> away). As recommended on the mailinglist I used iwrap for only one
>>>>> step:
>>>>>
>>>>> Wrap it
>>>>> &cntrl
>>>>> imin= 0, irest= 1, ntx = 5,
>>>>> ntb = 1,
>>>>> cut = 10,
>>>>> ntc = 2, ntf = 2, tol = 0.000001,
>>>>> ntt = 0,
>>>>> nstlim = 1, dt = 0.001,
>>>>> ntpr = 1, ntwx = 1, ntwr = 5,
>>>>> ioutfm = 1, iwrap = 1,
>>>>> &ewald
>>>>> dsum_tol = 0.000001,
>>>>> /
>>>>>
>>>>> The restart file produced by this run has about 50% of the solute
>>>>> outside the waterbox (when visualized in vmd). I can still carry on my
>>>>> MD-runs (with iwrap=0) after this, but I am worried about the new
>>>>> coordinates for the solute with respect the the water.
>>>>>
>>>>> However, when I do reimage in ptraj it seems to be ok:
>>>>> center :1-224
>>>>> image familiar
>>>>> trajout test.rst restart
>>>>>
>>>>> It must be said I use an octahedral water box. Both pmemd9 and 10
>>>>> yields the same results for me with this respect.
>>>>>
>>>>> To wrap it up:
>>>>> - should iwrap=1 with pmemd10 work when using a octahedral box ?
>>>>> - or should I use ptraj to reimage? if so, are the velocities ok ?
>>>>>
>>>>> I realise this is a topic that has been discussed on the mailinglist
>>>>> earlier and I apologise if my questions are redundant. I searched, but
>>>>> did not find a clear answer on this..
>>>>>
>>>>> Best regards,
>>>>> Lars Skjaerven
>>>>> University of Bergen, Norway
>>>>> -----------------------------------------------------------------------
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>>>>>
>>>>
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>>>
>>>
>>>
>>> --
>>> mvh Lars Skjærven
>>> Institutt for Biomedisin
>>> Universitetet i Bergen
>>>
>>
>>
>>
>> --
>> mvh Lars Skjærven
>> Institutt for Biomedisin
>> Universitetet i Bergen
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>
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-- 
===================================================================
Carlos L. Simmerling, Ph.D.
Associate Professor Phone: (631) 632-1336
Center for Structural Biology Fax: (631) 632-1555
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Stony Brook University E-mail: carlos.simmerling_at_gmail.com
Stony Brook, NY 11794-5115 Web: http://comp.chem.sunysb.edu
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