[gmx-users] heat apears
feenstra at chem.vu.nl
Mon Dec 1 08:51:05 CET 2003
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.
| | |
| _ _ ___,| K. Anton Feenstra |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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