[gmx-users] Problems when simulating a protein in its crystal matrix.

[Itamar Kass]

Hi All,

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 
concentration.

Also here is my mdp file:

integrator=md

dt=0.002; ps !

nsteps=2500000

; OPTIONS FOR BONDS

; Constrain control

constraints=all-bonds

; Do not constrain the start configuration

continuation= yes

; Type of constraint algorithm

constraint-algorithm=lincs

; OUTPUT CONTROL OPTIONS

; Output frequency for coords (x), velocities (v) and forces (f)

nstxout=100000

nstvout=100000

nstfout=100000

; Output frequency and precision for xtc file

nstxtcout=2500

xtc-precision=1000

; Energy monitoring

energygrps=Protein

nstenergy=1000

; NEIGHBORSEARCHING PARAMETERS

; nblist update frequency

nstlist=5

; ns algorithm (simple or grid)

ns-type=Grid

; nblist cut-off

rlist=0.8

; OPTIONS FOR ELECTROSTATICS AND VDW

; Method for doing electrostatics

coulombtype= Reaction-Field

rcoulomb = 1.4

epsilon_rf= 62

vdw-type= Cut-off

; cut-off lengths

rvdw-switch= 0

rvdw= 1.4

; Apply long range dispersion corrections for Energy and Pressure

DispCorr= no

; OPTIONS FOR WEAK COUPLING ALGORITHMS

; Temperature coupling

tcoupl= berendsen

; Groups to couple separately, time constant (ps) and reference 
temperature (K)

tc-grps= Proteinsolvent

tau-t= 0.10.1

ref-t= 300300

; Pressure coupling

Pcoupl= no

Pcoupltype= isotropic

; Time constant (ps), compressibility (1/bar) and reference P (bar)

tau_p=1.0

compressibility=4.5e-5

ref_p=1.0

; Do not generate velocities

gen_vel=no

; Center of mass control

nstcomm=10000

; Periodic boundary conditions

pbc=xyz

; Mode for center of mass motion removal

comm-mode=Linear

; Groups for center of mass motion removal

comm-grps=system


Thanks in advance,
Itamar.

-- 


"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
| Australia
|
| Tel: +61 3 9902 9376
| Fax: +61 3 9902 9500
| E-mail: Itamar.Kass at monash.edu
============================================

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