On Mon, Oct 06, 2025, Patil Pranita Uttamrao via AMBER wrote:
>
>I am currently facing an issue during the minimization step of my system
>with multiple chains in AMBER, which looks fine after system preparation
>using tleap without any error. The water box appears to be breaking apart,
>and I observe the formation of holes in the solvent box and after few steps
>the protein system is then moving out of the waterbox during equilibration
>itself. I am using *AMBER 16 with ff14SB forcefield using TIP3P water
>model.*
>
>*Below is the step1 minimization input file.*
>
>Protein
> &cntrl
> imin = 1,
> maxcyc = 1000,
> ncyc = 500,
> ntb = 1,
> ntr = 1,
> cut = 10.0
> /
>Hold the PROTEIN fixed
>500.0
>RES 1 397
>END
>END
>
>Could anyone please suggest what might be causing this issue or how to
>avoid the water box distortion during minimization?
Getting "holes" in the solvent is often the result of a bad initial density.
If you are using solvateBox or solvateOct from tleap, be sure to set the
closeness number to something like 0.8: that will have a better
initial starting density than the default.
In most cases, "bubbles" like this will go away once you go to equilibration
with constant pressure. So, don't worry too much about behavior during
minimization. And, following the initial procedures that Dan Roe
mentioned is also a good idea.
...good luck...dac
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Received on Tue Oct 07 2025 - 19:00:02 PDT
