[gmx-users] heat apears

[Anton Feenstra]

David van der Spoel wrote:

> On Fri, 28 Nov 2003 parinald at unsl.edu.ar wrote:
> 
> 
>>Thank ´s  Dallas and Anton:
>>    Now I  run g_energy to analyze temperature, presure and volume,  
>>started the simulation at 300 K and the size of the box was (2.5  2  2).
>>
>>My .mdp file is:
>>
>>cpp                 =  /lib/cpp
>>constraints         =  all-bonds
>>integrator          =  md
>>dt                  =  0.002        ; ps !
>>nsteps              =  500000        ; total 1000 ps.
>>nstcomm             =  1
>>nstxout             =  250
>>nstvout             =  1000
>>nstfout             =  0
>>nstlog              =  100
>>nstenergy           =  100
>>nstlist             =  10
>>ns_type             =  grid
>>rlist               =  0.5
>>rcoulomb            =  0.5
>>rvdw                =  0.5
> 
> 
> your cut-offs are too short. Make it 1 nm.

Or, rather, try a twin-range, like rlist=0.8, rcoulomb=1.2, rvwd=1.2.

For something like ATP with ions, you may want PME in stead of a cut-off.

Finally, be aware that temperature often can be a few degrees above
'ref_t', and that pressure fluctuations are *huge*, indeed as you already
saw they are on the order of 1000's of bar. The average pressure should
still be very close to 1, after a few 100ps.


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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