From: Nitin Bhardwaj (nbhardwaj_at_gmail.com)
Date: Sun Nov 13 2005 - 12:26:35 CST
Dear NAMD users,
I am simulating a small patch of lipid bilayer (of size x=35 y=39
z=88) with Amber force-filed (using prmtop and inpcrd files). This
inhomogenous patch was formed by removing four lipids (from the middle
of the one of the layer) and placing two bulkier lipids in their
place. That's why lipids in one layer were loosely placed as compared
to the lipids in another layer. Also, overall the lipids were a little
more losely placed as compared to the experimental values. I am
simulating in NPT ensemble, so I thought that the patch would contract
to the optimum size during the simulation. After 2000 steps of
minimisation, NAMD terminated giving the error:
Periodic cell has become too small for original patch grid.
Possible solutions are restart from a recent checkpoint, increase
margin, or disable useFlexibleCell for liquid simulation.
I did not have a checkpoint and did not want to disable
useFlexibleCell so I increased the margin. I read the manual about
margin but I could not get completely what does it mean. I,
nevertheless, set margin to 5 (default is 0). It did not give the
above error but after the minimisation it terminated giving the
Setting parameter binaryoutput from script failed!
binaryoutput was set to 'no' at that time.
Even after I set binaryouput to 'no', it still terminates saying the same error.
My questions are as follows:
1) what does margin signify? Do I need to keep something in mind
before I set it to a non-zero values?
2) why am I getting the error "Setting parameter binaryoutput from
script failed! "?
Is something wrong with my parameter setting, in light of the fact
that I am using amber force-field? I created the prmtop and inpcrd
files using amber 8.
I am running latest version of NAMD (windows version) on a fast XP machine.
I am attaching my configuration file.
I would appreciate it if anyone could find out the mistake in
Thanks a lot for any help in advance.
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