On 9/15/16 11:46 AM, soumadwip ghosh wrote:
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.
Loading two coordinate files in VMD and comparing them is not a rigorous
assessment. Most visualization programs are pretty notorious for simply
rendering secondary structure wrong. What does a real analysis, like DSSP or a
dihedral time series, tell you?
The corresponding C-alpha RMSD and radius of gyration are also fluctuating.
Could anyone help me understand what's going on?
RMSD and Rg will always fluctuate. A large, systematic drift would be a
problem. Fluctuation is not.
-Justin
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
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a
mail to gmx-users-requ...@gromacs.org.
