[gmx-users] Energy mimimization in AcOH box

[Aditi Borkar]

Thanx Justin.

I had tried that too. Using both parameters I get the same outcome. I
notice that increasing the emtol to 2000 (that effectively reduces the
number of steps my system undergoes before converging) retains most of
the structure. Should I change the dielectric constant of the solvent
because my system is highly charged ( -744 e). The topology parameters
from ASP side chain that I used are as follows:

[ moleculetype ]
; Name            nrexcl
ACA             3

[ atoms ]
;   nr       type  resnr residue  atom   cgnr     charge       mass
typeB    chargeB      massB
     1        CH3      1    ACA     CB      1          0     15.035   ; qtot 0
     2          C      1    ACA     CA      2       0.27     12.011
; qtot 0.27
     3         OM      1    ACA    OD1      2     -0.635    15.9994
; qtot -0.365
     4         OM      1    ACA    OD2      2     -0.635    15.9994   ; qtot -1

[ bonds ]
;  ai    aj funct            c0            c1            c2            c3
    1     2     2    gb_26
    2     3     2    gb_5
    2     4     2    gb_5

[ angles ]
;  ai    aj    ak funct            c0            c1            c2            c3
    1     2     3     2    ga_21
    1     2     4     2    ga_21
    3     2     4     2    ga_37

[ dihedrals ]
;  ai    aj    ak    al funct            c0            c1
c2            c3
    1     4     3     2     2    gi_1

-Aditi Borkar,
TIFR,
Mumbai, India



On Sat, Sep 12, 2009 at 5:35 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> 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
>
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