[gmx-users] Simulation using disiloxane as a solvent

Akbar Shaikh Akbar.Shaikh at sparcmail.com
Fri Dec 8 10:03:11 CET 2017

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.

Akbar Shaikh
+91 9767217767

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