[gmx-users] About the temperature coupling

[David]

On Thu, 2002-11-28 at 15:12, llshen wrote:
> 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
yes: here you generate velocities at 300 K.

> 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
> *********************************************
> 
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-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel
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