Dear all,We have currently switched from amber14 to amber16. I have run 10ns simulation via Amber16 using following command,
md_simulation.in==============polyA-polyT 10-mer: 100ps MD
&cntrl
imin = 0, irest = 1, ntx = 7,
ntb = 2, pres0 = 1.0, ntp = 1,
taup = 2.0,
cut = 10.0, ntr = 0,
ntc = 2, ntf = 2, iwrap = 1,
tempi = 300.0, temp0 = 300.0,
ntt = 3, gamma_ln = 1.0,
nstlim = 500000, dt = 0.002,
ntpr = 1000, ntwx = 500, ntwr = 1000
/
After 3ns, I tried to use ambpdb command to check the result, but I got following error message;| ambpdb (C++) Version V15.00
| Reading Amber restart from STDIN
Error: Could not read restart atoms/time.I read previous amber archive related to this issue and by following Daniel suggestion error is successfully resolved. I used following script for making pdb from rstambpdb -p file.prmtop -c md_simulatio3.rst > md3.pdb
Now the issue is I cannot see thetrajectories (mdcrd.gz file) using VMD. Could anybody let me know what went wrong? and why rst is in binary format? Output files of my job is perfectly fine.
Thankyou in advance.
Best,Saman
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Received on Mon Jan 02 2017 - 02:30:02 PST
