[gmx-users] Change in structure after solvation_Gromacs

[Justin A. Lemkul]

swagata chakraborty wrote:
> Hi,
> Thanks  a  lot for the reply and the suggestion.
> I am carrying the simulation in 100% DMSO( no water) at 318 K.the em.mdp 
> file is as follows:
> define              =  -DFLEXIBLE
> constraints         =  none
> integrator          =  steep
> dt                  =  0.002            ; time step
> nsteps              =  1000            ; number of steps
> nstlist             =  10            ; update pairlist
> ns_type             =  grid
> coulombtype         =  PME
> rcoulomb            =  1.0
> vdwtype             =  cut-off ;shift
> rlist               =  1.0            ; cut-off for ns
> rvdw                =  1.4
> 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
> emstep              =  0.01
> 
> 
> 
> DSSP is giving change in the sheet, loop and turn content although the 
> helix content remains the same on comparison with the native pdb. What 
> is more surprising is that though it is a homodimer the structure change 
> in the two monomers is not the same ( in one monomer the sheet is 
> extended while in the other it is not.
> Is it fine if I try to first energy minimize the structure in vacuum and 
> then solvate in DMSO box and run the MD without minimizing in DMSO 

That sounds like bad protocol.  You should do an energy minimization of the 
complete system, even if you don't like the results.  Incorrect output is 
indicative of something fundamentally wrong, perhaps within the force field itself.

> box. Also when I am trying  any other force field an error is coming 
> 'Atomtype SD not found'.

Force field files can't be mixed haphazardly.  Parameters are typically derived 
and distributed for one force field at a time.

>  For check I ran the MD of my protein in water using G43a1 forcefield, 
> in that also after em step the loop is turning into a beta sheet. 

As I recall, your original message said the problem initially appeared with 
53A6.  Comparing the results with 43A1 is not a very good test.  I know 53A6 is 
prone to giving extended configurations (per the literature), so likely 43A1 has 
some similarities, since bonded parameters are very similar.  A better test 
would be any one (or all) of OPLS-AA, AMBER, or CHARMM.  Of course, this 
requires proper DMSO parameters for these force fields, but no one ever said 
life was easy :)

> Please let me know if there is any manual on DMSO box generation and 
> equilibration. 
> 

There aren't how-to's for everything imaginable, but there is relevant 
literature.  A quick search will turn up the 53A6 DMSO parameters, which should 
be a reasonable starting point for whatever you want to learn.

-Justin

> Regards,
> Swagata Chakraborty
> Research Scholar,
> Department of Chemical Sciences,
> Tata Institute of Fundamental Research, 
> Mumbai-400005
> Swagata Chakraborty
> Research Scholar,
> Department of Chemical Sciences,
> Tata Institute of Fundamental Research,
> Mumbai-400005
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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