AMBER Archive (2008)

Subject: Re: AMBER: pmemd iwrap trouble

From: Lars Skjærven (lars.skjarven_at_biomed.uib.no)
Date: Tue Aug 26 2008 - 11:23:31 CDT

Hi Carlos,
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..

Cheers,
Lars

On Tue, Aug 26, 2008 at 4:26 PM, Carlos Simmerling
<carlos.simmerling_at_gmail.com> wrote:
> Hi Bob,
> no bonds, it is just a dimer with two separate molecules. I suspect
> that your code for deciding when to wrap and ptraj's are not quite the
> same, or something like that. ptraj and sander use the same- can you
> tell me how you wrap? is it deciding based on the first atom in the
> molecule, etc. Also I've already run the simulations (hundreds of ns
> for 4 systems) so rerunning isn't really an option, I need to find a
> way to properly image the current traj files.
> thanks
> carlos
>
> On Tue, Aug 26, 2008 at 12:38 AM, Robert Duke <rduke_at_email.unc.edu> wrote:
>> Carlos -
>> I did have one idea on what may be going on here. For pmemd 10 (I presume
>> what you are using), in order to support extra points efficiently, I
>> introduced a "no_intermolecular_bonds" option. The default value for this
>> is 1, and what happens then is any molecules (as defined in the prmtop)
>> which have been covalently bonded are redefined as 1 fused molecule. Now, if
>> ptraj treats these differently in wrapping, there could be grief (ie., a
>> difference in how the wrapping occurs). One option, as long as you are not
>> using an extra points forcefield, is to set no_intermolecular_bonds to 0 in
>> &cntrl, and then the molecule definition will match the prmtop (but this may
>> not be permitted if you have tip4p water for instance). The use of
>> no_intermolecular_bonds was absolutely essential for high scaling with extra
>> points ff's, though you really could do tip4p and tip5p without this nicety
>> (where you would run into problems is with stuff in gaff I believe). I
>> actually also believe it to be the better interpretation of the situation,
>> but clearly this could create a ptraj/pmemd inconsistency. So the critical
>> question - would you have any molecules that would be fused in your system?
>> 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 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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>>>>>>>> The AMBER Mail Reflector
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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
>>>>> -----------------------------------------------------------------------
>>>>> The AMBER Mail Reflector
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>>>>> to majordomo_at_scripps.edu
>>>>>
>>>>
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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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>>
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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
> ===================================================================
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
> to majordomo_at_scripps.edu
> 

-- 
mvh Lars Skjærven
Institutt for Biomedisin
Universitetet i Bergen
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