Hi,
On Thu, Jan 29, 2015 at 5:54 AM, Fabian Glaser <fabian.glaser.gmail.com> wrote:
> Related to this, is it necessary anymore to align trajectories made in separated ns runs before to restart a new ns run?
What exactly do you mean by 'aligning trajectories'? The only times
that I've ever needed to pre-process a coordinate file is autoimaging
when using restraints on systems with multiple molecules (e.g. DNA)
since restraints are not imaged.
> I noticed in the past that if I don't realign between ns, the initial energies and rmsd analysis of EACH ns production has a starting jump (slight destabilization) in values when trajin and analyzed. Is this solved by using ioutfm=1
I presume you're talking about RMSD to first trajectory frame? If so,
this RMSD jump is expected - it would actually be strange if the RMSD
stayed low. See the following article for a nice description of
expected RMSD distributions: Pitera, JPCB, 2014, 118, 6526-6530
(
http://pubs.acs.org/doi/abs/10.1021/jp412776d).
-Dan
> and ntxo=2 ??
>
> Thanks!!
>
> Fabian
>
>
> _______________________________
> Fabian Glaser, PhD
>
> Technion - Israel Institute of Technology
> Haifa 32000, ISRAEL
>
> fglaser.technion.ac.il
> Tel: +972 4 8293701
> Fax: +972 4 8225153
>
>> On Jan 29, 2015, at 2:42 PM, David A Case <case.biomaps.rutgers.edu> wrote:
>>
>> On Thu, Jan 29, 2015, Fabian Glaser wrote:
>>>
>>> I am trying to simulate a box with two drugs inside, they are the same
>>> molecule a figure is attached. I use iwrap in my eq stage , which I
>>> understand is the right way to go in multi stage simulations (eq or md
>>> production). But I get a warning about only one of the two molecules on
>>> the output file, every time a step details are written:
>>>
>>> ---------------------------------------------------
>>> wrapping first mol.: -42.08192 29.75641 51.53962
>>
>> This is just a piece of information; it is not a warning.
>>
>> If you are concerned about what is happening, viusalize the trajectory and
>> follow the path of the ligands.
>>
>> Setting iwrap is generally not needed anymore. Just be sure to set ioutfm=1
>> and ntxo=2.
>>
>> ....dac
>>
>>
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
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Received on Thu Jan 29 2015 - 08:30:02 PST
