AMBER Archive (2008)

Subject: Re: AMBER: pmemd iwrap trouble

From: Robert Duke (rduke_at_email.unc.edu)
Date: Mon Aug 25 2008 - 22:38:13 CDT


Hi Carlos -
Not a clue what is going on here. I have had nothing but grief on imaging
with ptraj, and as far as I know the sander and pmemd code are essentially
identical on imaging issues. I'll have to look into it; I suspect it is
some "way down in the decimals" minor problem, but still annoying. I
replicate trajectories for like 500 steps or so, so I am just not sure
what's up.
Regards - Bob
----- Original Message -----
From: "Carlos Simmerling" <carlos.simmerling_at_gmail.com>
To: <amber_at_scripps.edu>
Sent: Monday, August 25, 2008 12:35 PM
Subject: Re: AMBER: pmemd iwrap trouble

> 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 SkjŠrven"
>> <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 SkjŠrven
>>> <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 3┼ to 80┼
>>>> 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 SkjŠrven"
>>>>> <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 SkjŠrven
>>>> Institutt for Biomedisin
>>>> Universitetet i Bergen
>>>>
>>>
>>>
>>>
>>> --
>>> mvh Lars SkjŠrven
>>> 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
> CMM Bldg, Room G80
> 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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