AMBER Archive (2008)

Subject: Re: AMBER: pmemd iwrap trouble

From: Robert Duke (rduke_at_email.unc.edu)
Date: Mon Aug 25 2008 - 10:45:03 CDT

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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