[gmx-users] Energy mimimization in AcOH box

[Justin A. Lemkul]

Aditi Borkar wrote:
> Dear All,
> 
> Hello!
> 
> I am simulating a protein in a box of 9M acetic acid. I have obtained
> the coordinates and gromacs topology for AcOH from PRODRG. The AcOH
> has net -1 charge and the topology file is as follows:
> 

PRODRG topologies generally produce unsatisfactory charges.  For acetic acid, I 
would use the same charges found in an ASP side chain as a starting point.  You 
will note that your topology differs greatly from an ASP side chain in any of 
the Gromos96 force fields.

> [ moleculetype ]
> ; Name nrexcl
> ACA      3
> 
> [ atoms ]
> ;   nr      type  resnr resid  atom  cgnr   charge     mass
>      1       CH3     1 ACA     CAA     1    0.056  15.0350
>      2         C       1  ACA     CAD     1    0.393  12.0110
>      3        OM     1  ACA     OAC     1   -0.725  15.9994
>      4        OM     1  ACA     OAB     1   -0.724  15.9994
> 
> [ bonds ]
> ; ai  aj  fu    c0, c1, ...
>    1   2   1    0.153    334720.0    0.153    334720.0 ;   CAA  CAD
>    2   3   1    0.125    418400.0    0.125    418400.0 ;   CAD  OAC
>    2   4   1    0.125    418400.0    0.125    418400.0 ;   CAD  OAB
> 
> [ pairs ]
> ; ai  aj  fu    c0, c1, ...
> 
> [ angles ]
> ; ai  aj  ak  fu    c0, c1, ...
>    1   2   3   1    120.0       418.4    120.0       418.4 ;   CAA  CAD  OAC
>    1   2   4   1    120.0       418.4    120.0       418.4 ;   CAA  CAD  OAB
>    3   2   4   1    126.0       502.1    126.0       502.1 ;   OAC  CAD  OAB
> 
> [ dihedrals ]
> ; ai  aj  ak  al  fu    c0, c1, m, ...
>    2   1   4   3   2      0.0 1673.6        0.0 1673.6   ; imp   CAD
> CAA  OAB  OAC
> 
> When I had tried taking uncharged AcOH, during equilibration, the
> water and AcOH were completely segregating into two layers (like a
> biphasic system).
> 
> My problem arises when I perform energy mimization on my solvated
> protein. With 300 steps of EM (emtol 1000 and emstep .01) the EM
> doesn't converge and more distrurbingly within these few steps, the
> secondary structure of my protein is completely lost. This problem
> does not occur when I do EM in box containing protein and pure water.
> The Fmax is displayed onto 2 TRP residues.
> 

It is strange that this degree of change is occurring during EM.  But I wouldn't 
try anything else until you're sure you are starting with reasonable parameters 
(see above).

-Justin

> My em.mdp file is as follows:
> 
> define           =  -DFLEXIBLE
> constraints      =  none
> integrator       =  steep
> dt               =  0.002    ; ps !
> nsteps           =  300
> nstlist          =  10
> ns_type          =  grid
> rlist            =  0.9
> coulombtype      =  PME
> rcoulomb         =  0.9
> rvdw             =  0.9
> fourierspacing       = 0.12
> fourier_nx     =  0
> fourier_ny     =  0
> fourier_nz     =  0
> pme_order      =  4
> ewald_rtol     =  1e-5
> optimize_fft         =  yes
> ;
> ;      Energy minimizing stuff
> ;
> emtol              =  1000.0
> emstep             =  0.01
> 
> Please help!
> 
> Thank you!
> 
> -Aditi Borkar,
> Tata Institute of Fundamental Research,
> Mumbai,
> India.
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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================