Re: [AMBER] Calculation halted on pmemd.cuda

From: Carlos Simmerling <>
Date: Sun, 28 Mar 2021 07:25:19 -0400

it sounds like you have lots of additional parameters and a very complex
and challenging system. There are many things that could be going wrong. I
might start with the water. Generating a new water model can be very
involved and not as simple as most small molecules. Why not adjust the
buffer distance to get the desired number of water molecules instead of
making a whole new water model (which is an entire project on its own)?

On Sun, Mar 28, 2021 at 3:22 AM 库米尔 <> wrote:

> Dear Carlos
> Thanks Carlos for the prompt reply. Am trying to simulate coagulation
> of cellulose/[Bmim][Cl] ionic liquid solution to cellulose solid film in
> water and aqueous ethanol solution coagulants. The cellulose comes from
> GLYCAM website, generated ionic liquid. ethanol from Avogadro, did the
> optimization and RESP calculations on Guassian. RESP charges, frcmod,
> libraries with antechamber and xleap and finally packed the components with
> packmol to generated simulation box. The tip3p water model was not giving
> me the desired number of water molecules(4752) using the solvate function
> with buffer so I generated the water molecules, optimized and derived RESP
> charges similar to the other components described above. I hope the
> explanation has been thorough Sir?
> Alex
> _______________________________________________
> AMBER mailing list
AMBER mailing list
Received on Sun Mar 28 2021 - 04:30:02 PDT
Custom Search