On Wed, Nov 10, 2004, Daniel Wetzler wrote:
>
> NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS =********
> Etot = ************ EKtot = 0.0000 EPtot = ************
> BOND = 114.2394 ANGLE = 511.8678 DIHED = 1184.2036
> 1-4 NB = 823.3046 1-4 EEL = 12974.1609 VDWAALS = ************
> EELEC = -45507.8938 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 0.0000 VIRIAL = ************ VOLUME = 191472.4309
> Density = 0.7724
> Ewald error estimate: 0.6883E-04
You should never start a constant pressure simulation until the system
has been equilibrated to a good temperature using constant volume. Also, the
fact that your van der Waals potential is out of bounds at the first step
suggests that the system was not prepared correctly: you might want to
use the ptraj "checkoverlap" command to look for bad contacts.
>
> So it seems that AMBER 7 can't handle so many water molecules.
This probably has nothing to do with how many water molecules there are. It
is true that you can hide some problems by turning on belly, but you should
find out what is wrong with your system first.
.....dac
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Received on Wed Nov 10 2004 - 15:53:01 PST
