Hi all,
I came across a problem with my MD recently. The system is a membrane protein containing about 70,000 atoms and was simulated with AMBER11. The following is the input file of production phase.
production hSGLT2_dpp
&cntrl
imin=0,irest=1,ntx=5,
nstlim=5812000,dt=0.002,
ntc=2,ntf=2,
cut=10.0, ntb=2, ntp=2, taup=2.0,
ntpr=1000, ntwx=1000,
ntt=3, gamma_ln=2.0,
temp0=300.0,
/
When the job went to 38ns, some asterisks appear in the restart file. That leads to the impossibility of restarting the job. Now the only thing I can do is to avoid breaking the calculation. I copied some of the data in the rst file.
59.7272199************ 137.8027357 -59.5537208************ 138.0484368
60.4061406************ 138.4130880-156.4547856 88.0830801 142.243969
My question is:
Why did this problem arise and how should I fix it?
Many thanks!
╔════════════════════════╗
Cao Yang, Master,
Department of Medical Chemistry,
College of Pharmaceutical Sciences,
Zhejiang University,
Hangzhou, China
Email: muxiachuixue.163.com
╚════════════════════════╝
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Received on Mon Oct 08 2012 - 05:30:05 PDT
