Thanks!
Related to this, is it necessary anymore to align trajectories made in separated ns runs before to restart a new ns run?
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
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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Received on Thu Jan 29 2015 - 05:00:04 PST
