[gmx-users] About energy minimization problem of fatty acids.

[Haberl Florian]

> Dear all,
> I am new user of GROMACS. I'm triyng to run energy minimization for a
> mixture of fatty acid molecules using ffgmx. I have updated ffgmx.rtp,
> .hdb and aminoacids.dat files introducing these molecules. The charges are
> defined only for the -COOH group and 0.00 for rest of CH2 and CH3 grps.
> During energy minimisation I am getting convergence problem as :
>
>
> Steepest Descents converged to machine precision in 76 steps,
> but did not reach the requested Fmax < 1000.
> Potential Energy  = -1.60203164239929e+05
> Maximum force     =  1.84024599812275e+06 on atom 665
> Norm of force     =  5.30962675879254e+06
>
> I am getting same message with conjugate gradient method also.
> The resulted geometry shows -OH group to be detached from the residue
> molecules.
>
> I have changed the convergence criteria also. But then Potential Energy
> results to some high positive number.
>
> Can anyone help me in solving this problem?
>

have you tried l-bfgs algo too (see man p. 130) ?
you can also try to change to double precision version of gromacs tools,
so you get some better accurancy and perhaps lower potential energy.


my em.mdp looks like:

title               =  $date $time
cpp                 =  /lib/cpp
define              =  -DFLEXIBLE
constraints         =  none
integrator          =  l-bfgs
dt                  =  0.002    ; ps !
nsteps              =  10000    ; 20
nstlist             =  10
ns_type             =  grid
coulombtype         = Switch
vdw-type            = Switch
rlist               =  1.0
rcoulomb            =  0.9
rvdw                =  0.9
;
;       Energy minimizing stuff
;
emtol               =  100.0
emstep              =  0.005
epsilon_r           = 1


Greetings

Florian





------------------------------------------------------------------------
 Florian Haberl              Universitaet Erlangen/Nuernberg
 Computer-Chemie-Centrum     Naegelsbachstr. 25, D-91052 Erlangen

 Mailto: florian.haberl AT chemie.uni-erlangen.de

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