Your system starts with a very high initial density >1.1g/cm^3. Hence the
volume of your unit cell expands rapidly. This could just be the system
relaxing or it could be that something is blowing up due to instabilities
with the structure. Either way the rapid expansion of the unit cell is what
is giving you the ewald bomb message. You should be able to just restart the
simulation from that point and it will run. However, you should really take
a close look at the trajectory file and see if you can see anything
obviously wrong. You might also want to start at a lower temperature and
heat the system slowly. You may also want to see if you can work out why the
initial density is so high. If you want to lower the density slightly you
could edit the inpcrd file and increase the box dimensions slightly, at the
end of the file. Then run a short simulation with constant volume before
switching to constant pressure.
Running the initial phases of a simulation with slightly different settings
to other molecules shouldn't cause too many problems. You should be fully
equilibrating your systems anyway before 'collecting' results and so as long
as sufficient time has been allowed for equilibration and the protocoll used
for collecting phase is the same you shouldn't bias your results.
I hope this helps.
All the best
Ross
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|\oss Walker
| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel: +1 858 784 8889 | EMail:- ross.rosswalker.co.uk |
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From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf Of
S.Sundar Raman
Sent: Thursday, November 17, 2005 02:03
To: amber.scripps.edu
Subject: AMBER: need clarification on EWALD BOMB error
dear amber friends,
i am doing 1ns dynamics for some set of protein molecules whose AA sequence
varies at only one position. i did dynamics for 7 molecules and got the
results successfully by same procedure. when i repeat the same procedure for
8th molecule it produces EWALD BOMP error in equilibration process. i
searched the previous quires in the amber reflector sites it say i have to
change the conditions slightly like in the following amber page
http://amber.ch.ic.ac.uk/archive/200208/0170.html
i don't know, is it advisable to change the parameter for one calculation.
how much this parameter will affect the dynamics. please give some good
suggestion on this problem. i attached my output files also here for
equilibration process
--
S.Sundar Raman
Chemical Lab,
CLRI
Chennai-20
ph: 044-24411830
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Received on Thu Nov 17 2005 - 16:53:00 PST
