AMBER Archive (2008)

Subject: Re: AMBER: pmemd iwrap trouble

From: Lars SkjŠrven (
Date: Tue Aug 26 2008 - 13:36:06 CDT

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 1.6┼. 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 10┼" completely solvating my protein, instead I had to use "solvateoct 32┼" ( using only 10┼ left big chunks of my protein out of the waterbox. for any other proteins besides this big monster protein I have worked with, "solvateoct 10┼" 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 <> 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" <> > To: <> > 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 >> >> ----------------------------------------------------------------------- >> The AMBER Mail Reflector >> To post, send mail to >> To unsubscribe, send "unsubscribe amber" (in the *body* of the email) >> to >> > > ----------------------------------------------------------------------- > The AMBER Mail Reflector > To post, send mail to > To unsubscribe, send "unsubscribe amber" (in the *body* of the email) > to > ----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to To unsubscribe, send "unsubscribe amber" (in the *body* of the email) to