[EMAIL PROTECTED] wrote:
Dear colleagues,
I successfully finished a 3 ns gromacs run using 40
nodes. When, I tried to convert .trr file to .xtc using trjconv, the
run stops at 560 frame giving error "cannot determimine precision of
trn file". I tried various options like -skip, -b and -e, -dt option
as well as -ndx option . But, each time, the run stops at 560.
The second run I gave for 6 ns and this time, the
trjconv stops at 1180 frame. I have observed the .trr files occupying
huge memory space - 18 G for 3ns and 34 G for 6 ns runs respectively.
Memory is not a problem, as I have lot of disk space available.
As some guidelines,
1. Try to use XTC in first place; avoid using TRR unless for some
specific calculation.
2. Having a lot of disk space doesn't mean the latency is short and data
integrity is guaranteed. Check network traffic status if you are using
network file system like NFS.
3. Restart and continue simulation for every 1ns.
My system is a pentamer with 1052 residues and 47201 water
molecules.The simulation ran for 5 days.
I would be extremely thankful for any kind of suggestions in this regard.
Prema,
Graduate student,
University of Houston.
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