AMBER Archive (2004)

Subject: AMBER: positive VDWAALS

From: John (
Date: Sun Nov 07 2004 - 12:11:13 CST



I am in the process of equilibrating a protein of 153 residues in water. I
am using AMBER 8 and have followed the common protocol suggested in the
tutorial. At this stage the system has been equilibrated. As you can see
from the following snapshot everything seems normal apart from the VDWAALS
which is positive. It has been positive since the initial minimisation step.


NSTEP = 68300 TIME(PS) = 196.600 TEMP(K) = 302.25 PRESS =

 Etot = -62460.2017 EKtot = 15590.5659 EPtot =

 BOND = 447.6136 ANGLE = 1256.1947 DIHED =

 1-4 NB = 547.0522 1-4 EEL = 7323.9176 VDWAALS =

 EELEC = -98156.0252 EHBOND = 0.0000 RESTRAINT =

 EKCMT = 6872.6451 VIRIAL = 6198.9562 VOLUME =

                                                    Density =

 Ewald error estimate: 0.1461E-03



It seems that pairs of atoms have been trapped in proximity closer than the
sum of their VDW radii. I have tried different solvent (DMSO) and simulation
in implicit solvent as well as in vacuo. In all of these the VDWAALS is
negative. I have also taken the minimised structure from vacuo and then
solvated in water and I again get positive VDWAALS. I have used both water
boxes but still positive VDWAALS.


I would like to ask how critical this is for the simulation and how I could
overcome this issue.


Thanks for the help.



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