[gmx-users] stay at some temperature during annealing

[Dr. Vitaly Chaban]

On Tue, Jun 11, 2013 at 12:52 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 6/11/13 1:11 AM, mu xiaojia wrote:
>
>> Hi guys,
>>
>> I am using simulated annealing for my protein+water+Ion system, I tried to
>> let the system stay at some temperature for a while, e.g.: stay at 600k
>> from 3000ps to 10000 ps, then gradually cool it down to 298k, so my mdp is
>> like:
>>
>> annealing_time = 0 3000 10000 20000 0 3000 10000 20000 0 3000 10000 20000
>> annealing_temp = 298 600 600 298 298 600 600 298  298 600 600 298
>>
>>
>> however, error message is:
>>
>> Found 12 annealing_time values, wanter 9
>>
>> apparently, the "600 600" does not work, does anyone have any suggestion,
>> or I could only separate the simulation? Thanks very much!
>>
>>


There is a problem with the number of temperature coupling groups. You have
defined less than you expect, as the program requests only 9 values. So,
refer to the number of points to T annealing, which you do not list here.


Dr. Vitaly Chaban