Re: [AMBER] Free energy calculation and system crash

From: Carlos Simmerling <>
Date: Sat, 2 May 2020 19:44:52 -0400

Have you already removed the charge on the atoms for which you are removing
vdw? Also, there can be a discontinuity at endpoints, so many researchers
do not fully disappear atoms. Are you following the method in a specific
paper? Another option is to use a soft core treatment. Since we know very
little about how you are doing the perturbation it is difficult to help.

On Sat, May 2, 2020, 6:54 PM Sadaf Rani <> wrote:

> Dear Amber users
> Although this forum is for the problems related to Amber only and I am
> using gromacs for the moment, but I want to get your expert advice on
> the topic other than software. I also tried on the research gate but could
> not get any reply. I assume people here are experts in this area of
> research as well that's why I am posting my question to get an
> understanding of my problem.
> currently, I am I have a protein-ligand system for which I am doing TI
> calculation. During vdw removal, my system crashes and generates different
> PDB structures. It is assumed that this normally happens when the system is
> not well equilibrated however, I have a well-equilibrated system. I also
> reduced the time step to 1 fs but still the same problem when the lambda
> window gets closer to 1. I tried with h-bond constraints as well as with
> all bonds constraint but still could not solve the problem. My system gives
> lincs warning and then crashes.
> Could you please give some suggestions what else could I look for in my
> system to solve this problem.
> Thanks in advance.
> Sadaf
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Received on Sat May 02 2020 - 17:00:02 PDT
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