Dear Annie,
> I am trying to use check the density and temp after step 4.3
> by typing xmgr
> summary.density and summary.temp.
>
> While the temp is approaching 300 C, but the density raise
> from 1 to 100,
> does it indicate something wrong here? If yes, how to solve
> this problem?
These are implicit solvent GB simulations so why would you think that the
density would be relevant or even calculated? Take a look at the
summary.density file and things should be obvious:
0.000
0.100
0.200
It just lists the time, no density information. Then take a look at the
output file:
NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 298.54 PRESS =
0.0
Etot = -2707.4122 EKtot = 565.9592 EPtot =
-3273.3714
BOND = 19.8606 ANGLE = 94.8508 DIHED =
384.7276
1-4 NB = 146.3847 1-4 EEL = -355.4854 VDWAALS =
-360.9695
EELEC = 1384.2247 EGB = -4586.9649 RESTRAINT =
0.0000
Oh look, no density there either...
Please don't just rely on the output from a simple perl script that one of
us has written to make life a little easier. You should always check the
output for yourself. Especially when things don't look right. And then once
you have done that just stop for a few minutes, switch off the computer
screen and think about things carefully...
All the best
Ross
/\
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|\oss Walker
| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
|
http://www.rosswalker.co.uk | PGP Key available on request |
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Received on Sun Sep 03 2006 - 06:07:10 PDT
