[gmx-users] Simulation using disiloxane as a solvent

Mark Abraham mark.j.abraham at gmail.com
Fri Dec 8 12:08:45 CET 2017


Sounds like your model isn't stable at a 1ns time step (which is normal,
try 0.5fs, but really whoever parametrized it should have directed your
choice). Nor is your density correct (so be gentle with the time step,
while using berendsen coupling).


On Fri, Dec 8, 2017, 8:03 PM Akbar Shaikh <Akbar.Shaikh at sparcmail.com>

> Dear Gromacians,
> I am trying to simulate a system containing a few lipids
> Phosphatidylcholine and DOTAP (+ve charged) in disiloxane as a solvent. The
> system works fine when I run NVT simulation with bond constraints(LINCS,
> all-bonds,1ns), but as soon as I remove the constraints and continue the
> NVT simulation it halts in between.
> Further I tried NPT instead of NVT to continue the simulation with
> constraints (LINCS,all-binds,1ns), it throwed a lot of LINCS warning and
> halted.
> Further I tried simulating the same system in a fresh run in Water instead
> of disiloxane and everything(NVT as well as NPT) works fine.
> Further I tried simulating disiloxane alone in a fresh run in a 3X3X3 box
> and that too works fine (both in NVT and NPT)
> Any suggestion on what can be done to solve the problem. I need to do a
> final NPT production run on my system once the error is resolved.
> Sincerely,
> Akbar Shaikh
> +91 9767217767
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