[gmx-users] Change in structure after solvation_Gromacs

[swagata chakraborty]

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 box. Also
when I am trying  any other force field an error is coming 'Atomtype SD not
found'.
 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.
Please let me know if there is any manual on DMSO box generation and
equilibration.

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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20101207/bb04f6ac/attachment.html>