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.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.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 Skjærven
Institutt for Biomedisin
Universitetet i Bergen
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Received on Wed Aug 27 2008 - 06:07:26 PDT
