Re: [AMBER] Free energy calculation and system crash

From: Sadaf Rani <>
Date: Sun, 3 May 2020 01:29:43 +0100

Dear Carlos
I am following the paper
yes, I have removed charge on the system before removing the vdw and
keeping the one distance, two angles, and three dihedral restraints on as
mentioned in the reference paper. During decoupling, I have softcore
potentials in my simulation.
I would be really grateful for your help in fixing this problem I am facing
since long.



On Sun, May 3, 2020 at 12:45 AM Carlos Simmerling <> wrote:

> 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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> > AMBER mailing list
> >
> >
> >
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Received on Sat May 02 2020 - 18:00:02 PDT
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