Re: AMBER: pmemd iwrap trouble

From: Lars SkjŠrven <lars.skjarven.biomed.uib.no>
Date: Mon, 25 Aug 2008 15:32:26 +0200

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 3┼ to 80┼
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 SkjŠrven"
> <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 SkjŠrven
Institutt for Biomedisin
Universitetet i Bergen
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Received on Wed Aug 27 2008 - 06:07:26 PDT
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