AMBER Archive (2008)

Subject: Re: AMBER: pmemd iwrap trouble

From: Robert Duke (rduke_at_email.unc.edu)
Date: Mon Aug 25 2008 - 23:22:44 CDT

Hi Lars,
Well, not sure this was much help, as I just realized I misspoke. The
"ioutfm" variable controls only the coordinate trajectory (mdcrd) and
velocity (mdvel) files format. As of amber 10 I believe, there is no way to
write the restrt file in a binary format. Prior to amber 10, you could use
the "ntxo" variable to control the format of the restart file, and there was
a binary format available, but since it was a fortran binary format, there
were a lot of headaches with portability. So the only possible restart
format in amber 10 is formatted text, and from a practical point of view,
that is what was best to use earlier. SO you should be getting proper
wrapping with iwrap for the restart file regardless of the value of ioutfm.
I do this sort of thing (wrapping) all the time with orthogonal unit cells,
but I don't that often run a truncated octahedron unit cell, so I will have
to poke around a bit to see if there is some imaging irregularity for that
case; I am not really "at work" until Wed, but will try to jump on this then
and check out pmemd vs. sander on all this wrapping stuff. It should all be
fine; all this sort of stuff in pmemd was originally taken from sander in
amber 6. You may want to send me (directly) some of your system files so I
can debug your specific case. Sorry for all the confusion; probably should
have waited until I was really back at work...
Best Regards - Bob
----- Original Message -----
From: "Lars Skjærven" <lars.skjarven_at_biomed.uib.no>
To: <amber_at_scripps.edu>
Sent: Monday, August 25, 2008 6:03 PM
Subject: Re: AMBER: pmemd iwrap trouble

> Hi again,
> thanks for helping me on this issue. :-)
>
> I'll turn to binary restart files to resolve my overflow problem
> then.. There is obviously something vital I am not getting as I cant
> get the binary restart files to work. In the input file I add
> "ioutfm=1", and I successfully get the trajectory file in binary
> format, but my restart file is still formatted.. should I still
> specifiy "-r restrt"? do I need "ntwv = -1" in my mdin-file? Are the
> the coordinate and velocity sets included in the mdcrd file when I use
> "ioutfm=1"? If so, what is the flag used for restarting a run? "-c
> mdcrd" as with formatted? Sorry for all the questions.. I am just
> slightly confused about the binary restart files now. and all my
> trying and failing is a bit frustrating =)
>
> Cheers,
> Lars
>
>
> On Mon, Aug 25, 2008 at 5:45 PM, 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
>>>>>> -----------------------------------------------------------------------
>>>>>> 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
>>>>>>
>>>>>
>>>>> -----------------------------------------------------------------------
>>>>> 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
>>>>
>>>
>>>
>>>
>>> --
>>> mvh Lars Skjærven
>>> Institutt for Biomedisin
>>> Universitetet i Bergen
>>> -----------------------------------------------------------------------
>>> 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
>>>
>>
>> -----------------------------------------------------------------------
>> 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
> -----------------------------------------------------------------------
> 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
>

-----------------------------------------------------------------------
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