Dear Amber experts
I am a new user of AMBER. I am trying to run a MD simulation following the tutorial on simulating a DNA polyA-polyT Decamer. I got a problem at the heating stage. I used the SHAKE algorithm (the same as in the tutorial), but the MD only ran for 7 steps (stepsize 1fs) and stopped with the error message of segmentation fault. At the step 7, the kinetic energy term becomes NaN. On the other hand, if I don't use the SHAKE algorithm (ntc=1, ntf=1, time step=0.2 fs) the MD ran normally. Any hints on this?
I also check the 6 step MD results using VMD, it seemed only a small part of the whole water was moving. I followed strictly the tutorial. The partial and full minimization went smoothly. I compared the structures before and after minimization, they looked just fine.
Thanks!
Best wishes
JT
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Received on Sat Jul 20 2013 - 13:30:03 PDT
