[gmx-users] Free energy perturbation of ligand

[Alessandra Villa]

Hi,

On Wed, Feb 12, 2020 at 8:54 AM TIASHA ADHIKARY <tiasha18 at iitg.ac.in> wrote:

> Hello,
> I am trying to calculate FEP using gromacs. I have used pmx for initial
> structure and .itp file.
> I am getting the following warning
>
> WARNING 1 [file MOL.itp, line 185]:
>   Some parameters for bonded interaction involving perturbed atoms are
>   specified explicitly in state A, but not B - copying A to B
>
> Even if I ignore this warning, structure is not minimizing.
>
> "Steepest Descents converged to machine precision in 185 steps,
> but did not reach the requested Fmax < 100.
> Potential Energy  =  1.8540598e+08
> Maximum force     =  5.4468039e+04 on atom 6
> Norm of force     =  2.0960916e+03"
>
> My guess is that your problem is in energy minimization step and not in
free energy calculation (NOTE I am not familiar with pmx). The warning does
not affect your energy minimization.
If you  perform the energy minimization without state B, you should get the
same.
To solve the problem, you could modify energy minimization setting (maybe
you could use other methods or changing  the criteria - see below) or/and
check that there is not something "wrong" in your starting structure.

http://manual.gromacs.org/documentation/current/user-guide/mdp-options.html?highlight=steep#run-control

http://manual.gromacs.org/documentation/current/user-guide/mdp-options.html?highlight=steep#energy-minimization

Best regards
Alessandra



> I am not understanding how to solve this error. I will be highly obliged
> if anybody help me.
>
> Thanks in advance.
>
> Regards,
> Tiasha Adhikary
> M.Tech, IIT Guwahati
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