[gmx-users] heat apears

[David van der Spoel]

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.

>; Berendsen temperature coupling is on in two groups
>Tcoupl              =  berendsen
>tc-grps                    =  CL-  NA+         SOL
>tau_t               =  0.1        0.1  0.1
>ref_t               =  300        300  300
>; Energy monitoring
>energygrps          =  CL-  NA+  SOL
>; Isotropic pressure coupling is now on
>Pcoupl              =  berendsen
>Pcoupltype          = isotropic
>tau_p               =  0.5
>compressibility     =  4.5e-5
>ref_p               =  1.0
>; Generate velocites is off at 300 K.
>gen_vel             =  yes
>gen_temp            =  300.0
>gen_seed            =  173529 
>
>As a results the temperature comes up 40 K, the new box is (2.4  1.9  1.9) 
>and the presure curve goes from 1000 bar to –1000 bar (average 0.2 bar). 
>What I´m doing wrong?.
>                      Thank you.
>
>
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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