Hello dear members of the AMBER mailing list,
I have recently been forced to move from AMBER 14.12 to AMBER 16.
My simulations started crashing and I soon realized that a dramatic
increase in memory consumption was at fault.
I am using the NMR center of mass distance restraints and after the
version change a four window replica system jumped in
memory usage from ca. 900MB to 2800MB, no other parameters were changed.
I suspect this is due to a change that happened in AMBER 14.13. as I
think I had these
same problems about a year ago after that update without realizing the
problem was the increase in memory usage.
A colleague did further testing and compared the NMR restraint
simulation to one using no restraints and one using the new NFE
restraints with the following results:
pmd
only pmd with CoM-Distance and CoM-Dihedral: 755MiB memory
md
no restraints at all: 755MiB memory
bbmd
pmd and bbmd in 2x2 replica: 839MiB memory/replica
NMR
only CoM-Distance with disang file: 1642MiB memory
The difference from using CoM and diehedral restraints (755MiB) to the
NMR (1642MiB) is a mystery to me. I would like to use the NMR restraints
because of other drawbacks of the new NFE restraints.
If you have any idea what is going on or if this might be a bug, I would
love to talk to you.
Greetings,
Paul Westphälinger
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Received on Tue Feb 21 2017 - 06:00:03 PST
