[gmx-users] Problems when simulating a protein in its crystal matrix.
itamar.kass at monash.edu
Mon Oct 18 02:13:58 CEST 2010
I wish to simulate a protein in its crystal form. The crystal is a
triclinic box with a C2 symmetry. I have built the unit cell, which has
4 copies of the protein, and add some water on top of the ones in the
pdb. Then minimized and run positional restrained MD followed by a non
restrained MD. The system crashed after ~600ps reporting of LINCS errors.
Now I have minimized it before running; I have checked the topology and
could not find any error; I have also tried to run it in shake and the
system crashed as well; I also run the system in NVT without any success.
I guess this is a symptom to something like pressure problems, PBC
issues or bad topology, but I could not find it. I also looked for an
isolated water molecule which might have caused it, without any success.
So I hope someone else can come with the bright idea I don't have.
The rate of water and protein is ~1 protein to 300 water molecules, In
addition I add NaCl to neutralise the system and bring it to 0.1M
Also here is my mdp file:
dt=0.002; ps !
; OPTIONS FOR BONDS
; Constrain control
; Do not constrain the start configuration
; Type of constraint algorithm
; OUTPUT CONTROL OPTIONS
; Output frequency for coords (x), velocities (v) and forces (f)
; Output frequency and precision for xtc file
; Energy monitoring
; NEIGHBORSEARCHING PARAMETERS
; nblist update frequency
; ns algorithm (simple or grid)
; nblist cut-off
; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
rcoulomb = 1.4
; cut-off lengths
; Apply long range dispersion corrections for Energy and Pressure
; OPTIONS FOR WEAK COUPLING ALGORITHMS
; Temperature coupling
; Groups to couple separately, time constant (ps) and reference
; Pressure coupling
; Time constant (ps), compressibility (1/bar) and reference P (bar)
; Do not generate velocities
; Center of mass control
; Periodic boundary conditions
; Mode for center of mass motion removal
; Groups for center of mass motion removal
Thanks in advance,
"In theory, there is no difference between theory and practice. But, in practice, there is." - Jan L.A. van de Snepscheut
| Itamar Kass, Ph.D.
| Postdoctoral Research Fellow
| Department of Biochemistry and Molecular Biology
| Building 77 Clayton Campus
| Wellington Road
| Monash University,
| Victoria 3800
| Tel: +61 3 9902 9376
| Fax: +61 3 9902 9500
| E-mail: Itamar.Kass at monash.edu
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the gromacs.org_gmx-users