Re: AMBER: pmemd iwrap trouble

From: Lars SkjŠrven <lars.skjarven.biomed.uib.no>
Date: Mon, 25 Aug 2008 16:58:01 +0200

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.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.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.biomed.uib.no>
>> To: <amber.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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Received on Wed Aug 27 2008 - 06:07:28 PDT
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