Dear yip,
Instead of iwrap=1 you can use
ioutfm=1, { The format of coordinate and velocity trajectory files (mdcrd, mdvel and inptraj) in Binary NetCDF format}
ntxo=2, { to create NetCDF restart file }
best,
Nitin
-----Original Message-----
From: Yew Mun Yip [mailto:yipy0005.gmail.com]
Sent: Thursday, February 27, 2014 11:11 PM
To: AMBER Mailing List
Subject: [AMBER] Unable to read coords from XXX.rst - How can I resolve this once and for all?
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 - 08:00:04 PST
