[gmx-users] About the temperature coupling

[Pedro Alexandre Lapido Loureiro]

Citando llshen <llshen at mail.shcnc.ac.cn>:

> Dear Lists:
> As suggested, I heated up my system (containing SPC water molecular) step by
> step with step width 100K or some value else. When I checked the temperature
> curves, however, I found that at every step the temperature was first up to
> hear 300K and then cool down to the refer temperature I choosed. It forms a
> heating up shock on the system in very short period, and I think such shock
> makes the step by step heating up strategy meaningless.  Did anyone else note
> this phenomenon or is it an operation error of mine?  If not my errors,
> what's the intrinsic explaination to this? 
> BTW, a sample of heating up *.mdp file is copied here:
> ;
> ;	User spoel (236)
> ;	Wed Nov  3 17:12:44 1993
> ;	Input file
> ;
> title               =  Yo
> cpp                 =  /lib/cpp
> define              =  -DPOSRES
> constraints         =  h-bonds
> integrator          =  md
> dt                  =  0.002	; ps !
> nsteps              =  50000	; total 100 ps.
> nstcomm             =  1
> nstxout             =  500
> nstvout             =  1000
> nstfout             =  0
> nstlog              =  100
> nstenergy           =  10
> nstlist             =  10
> ns_type             =  grid
> rlist               =  1.0
> rcoulomb            =  1.0
> rvdw                =  1.0
> ; Berendsen temperature coupling is on in two groups
> Tcoupl              =  berendsen
> tc-grps		    =  Protein	SOL  
> tau_t               =  0.1	0.1 
> ref_t               =  0	100  
> ; Energy monitoring
> energygrps	    =  Protein	SOL
> ; Pressure coupling is not on
> Pcoupl              =  no
> tau_p               =  0.5
> compressibility     =  4.5e-5
> ref_p               =  1.0
> ; Generate velocites is on at 300 K.
> gen_vel             =  yes
> gen_temp            =  300.0
> gen_seed            =  173529
> 
> Any suggestions?
> 
> Lingling Shen 
> ********************************************
> Lingling Shen        		(Ph.D Student)
> Drug Discovery and Design Center
> Shanghai Institute of Materia Medica
> Chinese Academy of Science
> Shanghai 200031, China
> 
> Tel. 086-021-64311833-222
> E-Mail: llshen at mail.shcnc.ac.cn
> *********************************************
> 

I think the problem is you are using
> gen_vel             =  yes
  gen_temp            =  300.0

Cheers

--
Pedro Alexandre Lapido Loureiro
Laboratório de Física Biológica
Instituto de Biofísica
UFRJ
Brasil