From: ydhuang2727 (ydhuang2727_at_163.com)
Date: Wed Nov 26 2008 - 20:54:30 CST
I add three types of water molecules as one expert suggested.
1)using DOWSER to inlay crystal water
2) SOLVATE progam constructed by Helmut Grubm¨ıller and Volker Groll to add a water layer and ions mediating PH value.
3) VMD solvate1.2 to add water box(-t 10).
Aboved should be right.
Two annoying problems occurred frequently that i thought the two are correlevant.
1) periodic cell has become too small for original patch grid!
2)Constraint failure in RATTLE algorithm for atom X( X denotes atom ID, which is close to the trouble Ligand), simulation has become unstable.
I have some information that may be useful to you:
If add first two kinds of water only and don't add water box, it means in NVE ensemble and everything is ok!
If not, it's in NTP ensemble and errors occur.
I have ever tried fixing all atoms except Ligand ( an small chemical molecule, C14 H12 F N5 O S2 ), and let it run to see what hell happen to the molecule. In the .log file, all energy items come to an stable value except for VDW item which stays 99999.9999. It seems to me that the ligand is tightly constrainted in the protein(but another one smaller ligand C6H12O6 in another binding site of the protein is ok ) and can't relax into a comfortable state owing to the pressure of water environment or something else.
I setup the CellBasicVectorX,Y, and Z ritht according to water box's length, width, and height, and
PMEgridSize, as you have suggested, is a litte larger than CellBasicVector.
The following is part of my .conf file, please have a look.
# Force-Field Parameters
# Integrator Parameters
timestep 2.0 ;# 2fs/step
rigidBonds all ;# needed for 2fs steps
# Constant Temperature Control
langevin on ;# do langevin dynamics
langevinDamping 5 ;# damping coefficient (gamma) of 5/ps
langevinHydrogen off ;# don't couple langevin bath to hydrogens
# Periodic Boundary Conditions
cellBasisVector1 91.431 0. 0.
cellBasisVector2 0. 102.25 0.
cellBasisVector3 0. 0. 94.117
cellOrigin 29.613 1.421 69.901
# PME (for full-system periodic electrostatics)
# Constant Pressure Control (variable volume)
useGroupPressure yes ;# needed for rigidBonds
langevinPistonTarget 1.01325 ;# in bar -> 1 atm
Can you find sth. wrong?!
If my depiction is not clear enough, will please help me confirm some words.
1) periodic cell has become too small for original patch grid(what's original patch grid)!
2)Constraint failure(what may happen to this constraint failure?) in RATTLE algorithm for atom X( X denotes atom ID, which is close to the trouble Ligand), simulation has become unstable
Thanks for your kind consideration and look forward to your quick reply!!
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