[gmx-users] Fwd: protein getting unfolded in SPC/E water

[soumadwip ghosh]

---------- Forwarded message ----------
From: soumadwip ghosh <soumadwipghosh at gmail.com>
Date: Thu, Sep 15, 2016 at 9:16 PM
Subject: protein getting unfolded in SPC/E water
To: "gromacs.org_gmx-users" <gromacs.org_gmx-users at maillist.sys.kth.se>


Hello,
         I am simulating Lysozyme in pure SPC/E water for 200 ns. I am
using OPLS-AA force field for my work. In pure water the protein looses
some of its helices. As for example in the final md.gro file the number of
alpha helices observed are 2 while in the beginning 4 were observed in VMD.
The corresponding C-alpha RMSD and radius of gyration are also fluctuating.
Could anyone help me understand what's going on?
I am pasting the snippets of my topology and the md.mdp files.


; Include water topology
#include "oplsaa.ff/spce.itp"

#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct       fcx        fcy        fcz
   1    1       1000       1000       1000
#endif

; Include topology for ions
#include "oplsaa.ff/ions.itp"

[ system ]
; Name
Protein in water

[ molecules ]
; Compound        #mols
Protein_chain_A     1
SOL         11071
CL               9
Here is the md.mdp one

constraints     = all-bonds     ; all bonds (even heavy atom-H bonds)
constrained
lincs_iter      = 1             ; accuracy of LINCS
lincs_order     = 4             ; also related to accuracy
; Neighborsearching
ns_type         = grid          ; search neighboring grid cells
nstlist         = 5             ; 10 fs
rlist           = 1.0           ; short-range neighborlist cutoff (in nm)
rcoulomb        = 1.0           ; short-range electrostatic cutoff (in nm)
rvdw            = 1.0           ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype     = PME           ; Particle Mesh Ewald for long-range
electrostatics
pme_order       = 4             ; cubic interpolation
fourierspacing  = 0.16          ; grid spacing for FFT
; Temperature coupling is on
tcoupl          = V-rescale     ; modified Berendsen thermostat
tc-grps         = SYSTEM        ; two coupling groups - more accurate
tau_t           = 0.1           ; time constant, in ps
ref_t           = 310           ; reference temperature, one for each
group, in K
; Pressure coupling is on
pcoupl          = Parrinello-Rahman     ; Pressure coupling on in NPT
pcoupltype      = isotropic     ; uniform scaling of box vectors
tau_p           = 2.0           ; time constant, in ps
ref_p           = 1.0           ; reference pressure, in bar
compressibility = 4.5e-5        ; isothermal compressibility of water,
bar^-1
; Periodic boundary conditions
pbc             = xyz           ; 3-D PBC
; Dispersion correction
DispCorr        = EnerPres      ; account for cut-off vdW scheme
; Velocity generation
gen_vel         = no            ; Velocity generation is off
energygrps      = protein SOL

I am quite sure that the system is well equilibrated.

Here is the part of md.edr file

Back Off! I just backed up energy.xvg to ./#energy.xvg.2#
Last energy frame read 75000 time 150000.000

Statistics over 75000001 steps [ 0.0000 through 150000.0000 ps ], 4 data
sets
All statistics are over 15000001 points

Energy                      Average   Err.Est.       RMSD  Tot-Drift
------------------------------------------------------------
-------------------
Temperature                 310.004     0.0015    1.64028 0.000388793  (K)
Pressure                    1.04308    0.00049    143.118 0.00201836  (bar)
Volume                      351.008     0.0063   0.835859  0.0314951  (nm^3)
Density                     1012.78      0.018    2.41171 -0.0908186
 (kg/m^3)


What might go wrong?
Thanks for your time in advance.

Soumadwip Ghosh
Senior Research Fellow
Indian Institute of Technology Bombay
India