Hi Nitin,
Thanks for the prompt reply, but I’m using amber 10, can I still use ioutfm and ntxo?
Regards
Yip Yew Mun
Graduate, PhD
Chemistry and Biological Chemistry
School of Physical and Mathematical Sciences
Nanyang Technological University
On 27 Feb, 2014, at 11:58 pm, Nitin Sharma <sharmanitin.nus.edu.sg> wrote:
> 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 _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Feb 27 2014 - 08:30:02 PST
