[gmx-users] Increase temperature to 550K

[Justin A. Lemkul]

Chih-Ying Lin wrote:
> Hi
> Here is the dt and constraints.
> Any other suggestion about heating up the system  and make the system stable?
> 

Like anything else, thorough equilibration under the desired conditions.

-Justin

> 
> Thank you
> Lin
> 
> 
> 
> 
> dt = 0.001
> 
> ; OPTIONS FOR BONDS
> constraints              = all-bonds
> constraint-algorithm     = Lincs
> unconstrained-start      = yes
> lincs-order              = 4
> lincs-iter               = 1
> lincs-warnangle          = 30
> 
> 
> 
> 
> Chih-Ying Lin wrote:
>> HI
>> The simulation system is merely water + one lysozyme.
>> I increase temperate to 550K.
>>
>> Then, the simulation broke.
>> The following message is shown.
>>
>> MX:hpc0011:Remote endpoint is closed, peer=00:60:dd:48:14:5b (hpc0010:0)
>> mpiexec: Warning: task 0 exited with status 1.
>> mpiexec: Warning: tasks 1-2 died with signal 9 (Killed).
>> mpiexec: Warning: task 3 died with signal 11 (Segmentation fault).
>>
>>
>> Anything wrong with the simulation?
>>
> 
> I think, pretty clearly, yes.  Increasing to a high temperature can make the
> system unstable.  Are you using a suitable dt?  Constraints?
> 
> -Justin
> 
>> Thank you
>> Lin

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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