[AMBER] Free energy calculation and system crash

From: Sadaf Rani <sadafrani6.gmail.com>
Date: Sat, 2 May 2020 23:54:14 +0100

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.

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Received on Sat May 02 2020 - 16:00:02 PDT
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