[gmx-users] Steepest Descents converged to machine precision

[nitu sharma]

Dear Mark

I explain you what I  want to ask . I give you a detail of my processing -
* step for packing lipid around protein-
1. concatanation of protein and lipid bilayer in proper orientation- I did.
2.Inflate the bilayer by using inflategro script with scaling factor 4 and
cutoff 14- I did .
 there is 8 lipid removed in this process and a/c to that   I have update my
topology file .
3. Energy minimisation by applying strong position restrain on protein the
force constant=100000

problem occur here is-

Step=  344, Dmax= 1.8e-05 nm, Epot=  4.29315e+06 Fmax= 1.02525e+05, atom=
4615
Step=  349, Dmax= 1.4e-06 nm, Epot=  4.29315e+06 Fmax= 9.86524e+04, atom=
4615
Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax < 1000

Double precision normally gives you higher accuracy.

writing lowest energy coordinates.

Steepest Descents converged to machine precision in 350 steps,
but did not reach the requested Fmax < 1000.
Potential Energy  =  4.2931510e+06
Maximum force     =  1.0252509e+05 on atom 4615
Norm of force     =  1.3668822e+03

my em.mdp file-
cpp                 =  /usr/bin/cpp
define              =  -DPOSRES
constraints         =  none
integrator          =  steep
nsteps              =  10000
;
;       Energy minimizing stuff
;
emtol               =  1000
emstep              =  0.001

nstcomm             =  1
ns_type             =  grid
rlist               =  1
rcoulomb            =  1.0
rvdw                =  1.0
Tcoupl              =  no
Pcoupl              =  no
gen_vel             =  no
comm-mode           = Linear
pbc                 = XYZ

my topology file is like this-
; Include forcefield parameters
#include "ffG53a6_lipid.itp"

#include "topol_A.itp"
#ifdef POSRES
#include "posre_A.itp

#include "topol_B.itp
#ifdef POSRES
#include "posre_B.itp
#endif

; Include DMPC chain topology
#include "dmpc.itp"

[ system ]
; Name
Protein in DMPC bilayer

[ molecules ]
; Compound        #mols
Protein_A           1
Protein_B           1
DMPC               120

my question-
1. probable reason of steepest descent converged to macine precision  but
did not reach the requested Fmax < 1000.
2.The even after applying strong position restrain on protein the protein
structure being disturbed.

If u can make help for me . I will appreciate you.

Thanks
Nitu sharma
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