In amber 10 you can use ioutfm=1, but not ntxo=2.
-Dan
> On Feb 27, 2014, at 9:05 AM, Yip Yew Mun <yipy0005.gmail.com> wrote:
>
> 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 _______________________________________________
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Received on Thu Feb 27 2014 - 08:30:04 PST
