AMBER Archive (2008)

Subject: Re: AMBER: pmemd iwrap trouble

From: Robert Duke (rduke_at_email.unc.edu)
Date: Tue Aug 26 2008 - 14:49:18 CDT

You might try wrapping in 1 step of 0.01 fsec (ie., dt = .00001). That way
the before and after delta in all atom positions should be reduced 100-fold,
and you should see a smaller energy delta. You would expect some
difference, as you are really minimizing two structures that differ by more
than just the wrapping operation - they also differ by the distance moved by
all atoms in the dynamics step. Also, using the 32 angstom water buffer
sounds pretty excessive. Is your protein complex perhaps not a good
candidate for fitting in a truncated octahedron? (so a globular protein
approximating a sphere is the best candidate; elongated structures may fit
better in an orthogonal unit cell). Also note my earlier comments about
no_intermolecular_bonds.
Regards - Bob

----- Original Message -----
From: "Lars Skjærven" <lars.skjarven_at_biomed.uib.no>
To: <amber_at_scripps.edu>
Sent: Tuesday, August 26, 2008 2:36 PM
Subject: Re: AMBER: pmemd iwrap trouble

> Hi Tom,
> I performed a 1 step energy minimization of the restart files before
> and after the wrapping in pmemd10. The energies are indeed similar,
> but not identical: -2.1748E+06 and -2.1750E+06.
>
> When I do "image center familiar" in ptraj of the restart files before
> and after pmemd wrapping, and then an rmsd in ptraj of the two new
> restart files, it gives an rmsd of 1.6Å. visualizing in vmd shows that
> most of the protein aligns, but two subunits are translated slightly
> with respect to the 10 other subunits.
>
> Ptraj scripts used:
> ---
> trajin b4_wrapping.rst
> trajin after_wrapping.rst
> center :1-6456
> image center familiar
> trajout reimaged.rst restart
> ----
>
> and then,
> ---
> trajin reimaged.rst.1
> trajin reimaged.rst.2
> rms first mass out rmsd.dat @N,CA,C
> ----
>
> Yes, I am still concerned about the validity of my simulation.. :-)
>
> Do I have any other choice to tackle this overflow issue? Can I use
> ptraj to reimage the water back in the box (which works fine), and
> make a new restart file (which I assume do not contain velocities,
> right?), and copy the velocities from the old restart file (which are
> about to overflow)? then, use this new and edited restart file to
> continue my simulation?
>
> When I built my system I had trouble with "solvateoct 10Å" completely
> solvating my protein, instead I had to use "solvateoct 32Å"
> (http://structbio.vanderbilt.edu/archives/amber-archive/2008/1109.php).
> using only 10Å left big chunks of my protein out of the waterbox. for
> any other proteins besides this big monster protein I have worked
> with, "solvateoct 10Å" works fine. can my problem with wrapping have
> anything to do with this issue? probably not.. ?
>
> Thanks for all help on this issue.
>
> Best regards,
> Lars Skjaerven
> University of Bergen, Norway
>
>
> On Tue, Aug 26, 2008 at 6:59 PM, Robert Duke <rduke_at_email.unc.edu> wrote:
>> Hi Tom,
>> Thanks, that was my understanding that the imaging in sander and pmemd
>> was
>> the same, and "equivalent" to a truncated octahedron, but that the image
>> would not look correct in something like vmd. I was hoping to get Tom D.
>> to
>> comment on this since he did the code. I don't use truncated octahedrons
>> that much myself, but have had 0 problems with other imaging, aside from
>> problems with not being quite sure what to do in ptraj sometimes, and
>> also
>> ptraj understandably can't keep up with box size changes associated with
>> a
>> constant pressure simulation (so wrapping a whole trajectory rather than
>> a
>> frame really blows up; one might expect that...). Anyway, thanks for the
>> input. I am going to confirm that my code is identical to sander in
>> amber
>> 10 with regard to wrapping, but that is what I expect. There IS a known
>> problem with the amber 9 release of pmemd, for which a patch was
>> released,
>> so some folks with an unpatched version of 9 may see a few molecules not
>> wrap correctly (so do the patch...).
>> Regards - Bob
>>
>> ----- Original Message ----- From: "Thomas Cheatham III" <tec3_at_utah.edu>
>> To: <amber_at_scripps.edu>
>> Sent: Tuesday, August 26, 2008 12:48 PM
>> Subject: Re: AMBER: pmemd iwrap trouble
>>
>>
>>>
>>>> I get exactly the same results from pmemd9, pmemd10, and sander10 in
>>>> regard the wrapping (iwrap=1); 2 of my subunits are displaced
>>>> (regardless of ioutfm=1 or 0). However, by using the following ptraj
>>>> script (instead of iwrap) it results in a truncated octahedral fitted
>>>> nicely around the protein complex (as expected):
>>>>
>>>> center :1-5332
>>>> image center familiar
>>>> trajout reimaged.rst restart
>>>>
>>>> However, I see no trouble when I use solvatebox instead of solvateoct
>>>> (for both sander and pmemd). Unfortunately I cant go back using
>>>> solvatebox at this time, after 2 months of simulations..
>>>
>>> I've been following this thread and think that it is just a
>>> misunderstanding and that nothing is wrong with the imaging, it just
>>> doesn't look like you would expect. sander/pmemd image in triclinic
>>> space
>>> so for a protein this looks like a slanted box with the protein
>>> potentially sticking out...
>>>
>>> __PPP__
>>> / PPP /
>>> /___PPP/
>>>
>>> ...rather than the more "familiar" truncated octahedron shape. To
>>> verify
>>> this, look at the ptraj imaged trajectory without the familiar keyword;
>>> this will look like what you are seeing from sander/pmemd and they are
>>> equivalent, albeit different ways of looking at things.
>>>
>>> There is also a way in pmemd to generate images in alternative unit
>>> cells,
>>>
>>> image xoffset 1.0 yoffset 0.0 zoffset 0.0
>>>
>>> which you can do for each direction and then "see" the whole packing in
>>> the unit cell.
>>>
>>> If you are still concerned, you could also try a single point energy
>>> minimization on both the "familiar" and alternative restrt file to
>>> verify
>>> the energies are similar.
>>>
>>> imaging in ptraj is not broken (now) to the best of my knowledge; there
>>> was a brief problem with AmberTools 1.0 that lead to errors in the box
>>> size, but this was working in earlier versions and is working in current
>>> versions.
>>>
>>> --tom
>>>
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>>
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