Hi, I have been trying to run a protein-drug simulation for at least 100 ns
using pmemd. However, after 50 ns, I received the error "Unable to read
coords from XXX.rst". I checked the trajectory and found that the water
have drifted way too far away.
I have read previous posts about setting iwrap=1 for running long
simulations with pmemd. But the manual indicates that running long
simulations with that setting will also result in consequences, therefore
with all the conflicting viewpoints, should I or should I not set iwrap=1?
What are the consequences if iwrap=1 is set for long simulations? If I
don't set iwrap=1, what can I do to continue the simulation correctly?
Many thanks, because I really hope to clear this once and for all. =D
--
Regards
Yip Yew Mun
Graduate, PhD
Chemistry and Biological Chemistry
School of Physical and Mathematical Sciences
Nanyang Technological University
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Received on Thu Feb 27 2014 - 07:30:04 PST
