[gmx-users] Lipids forming unsual bonds

[chris.neale at utoronto.ca]

"the lipids are forming usual cross bonds (seen in the form of long  
straight lines)"

lines? on what? You need to do a much better job of describing your  
problem and your observations before anyone can give you a better  
suggestion than "remove those lines and everything will be solved"...

That said, you're probably running into a regular pbc issue in vmd and  
you should then start with a .gro developed from trjconv -pbc mol or  
else you might try the "dynamic bonds" vmd representation. Otherwise,  
perhaps you are talking about loading in a post-equilibration .gro  
wherein the bond determination routine is finding "bonds" that don't  
make any sense and therefore your parameters or EM are probably bad.

Still, a better description gets better assistance.

Chris.

-- original message --

Hi ALL,

I am simulating a GPCR protein in a POPC bilayer.
I have followed Justins' tutorial to set up the system, but have used  
POPC instead of DPPC. I have used the same parameters given in that  
tutorial. Till equilibration everything went well. But after releasing  
the protein in the production MD, the lipids are forming usual cross  
bonds (seen in the form of long straight lines). How can I avoid this?  
Any suggestion is welcome.

Parameters used for MD:
--------------------------------------------------------------------------------------------------
title        = GPCR in POPC Production MD
; Run parameters
integrator    = md        ; leap-frog integrator
nsteps        = 500000    ; 2 * 500000 = 1000 ps (1 ns)
dt        = 0.002        ; 2 fs
; Output control
nstxout        = 1000        ; save coordinates every 2 ps
nstvout        = 1000        ; save velocities every 2 ps
nstxtcout    = 1000        ; xtc compressed trajectory output every 2 ps
nstenergy    = 1000        ; save energies every 2 ps
nstlog        = 1000        ; update log file every 2 ps
; Bond parameters
continuation    = yes        ; Restarting after NPT
constraint_algorithm = lincs    ; holonomic constraints
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 cels
nstlist        = 5        ; 10 fs
rlist        = 1.2        ; short-range neighborlist cutoff (in nm)
rcoulomb    = 1.2        ; short-range electrostatic cutoff (in nm)
rvdw        = 1.2        ; 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        = Nose-Hoover        ; More accurate thermostat
tc-grps        = Protein POPC    SOL_CL-    ; three coupling groups -  
more accurate
tau_t        = 0.1    0.1    0.1    ; time constant, in ps
ref_t        = 323     323    323    ; reference temperature, one for  
each group, in K
; Pressure coupling is on
pcoupl        = Parrinello-Rahman    ; Pressure coupling on in NPT
pcoupltype    = semiisotropic        ; uniform scaling of x-y box  
vectors, independent z
tau_p        = 2.0            ; time constant, in ps
ref_p        = 1.0    1.0        ; reference pressure, x-y, z (in bar)
compressibility = 4.5e-5    4.5e-5    ; isothermal compressibility, 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
---------------------------------------------------------------------------------------------------

Regards,

  Anirban GhoshGrade Based Engineer
Bioinformatics Team
Centre for Development of Advanced Computing (C-DAC)
Pune, India



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