[gmx-users] the temperature effect in the simulation

[He, Yang]

Hi Yuguang,

when I use the command ngmx to show the trajectory , I just choose the DNA group not including the water.

Any suggestions ? Thank you very much.

Yang
________________________________________
From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] On Behalf Of Mu Yuguang (Dr) [YGMu at ntu.edu.sg]
Sent: Tuesday, November 11, 2008 12:17 PM
To: Discussion list for GROMACS users
Subject: RE: [gmx-users] the temperature effect in the simulation

Do you have water ?

-----Original Message-----
From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org] On Behalf Of Nicolas Sapay
Sent: 2008年11月12日 4:15
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] the temperature effect in the simulation

He, Yang wrote:
> Hi all users,
>
> When I change the temperature to try to get different disassociation about the two DNA's strands. But even I change the value of temperature by 0K in the mdp file ,
>
> ; OPTIONS FOR WEAK COUPLING ALGORITHMS
> ; Temperature coupling
> Tcoupl                   = berendsen
> ; Groups to couple separately
> tc-grps                  = System
> ; Time constant (ps) and reference temperature (K)
> tau_t                    = 0.001
>
The coupling constant sounds a bit small. The dynamics of fast motions
may be affected more than you want, but I'm not a specialist of DNA and
I don't know if it's a problem in that particular case.
> ref_t                    = 300
>
This indicates that your target temperature is 300K not 0K
> ; Pressure coupling
> Pcoupl                   = no
> Pcoupltype               = isotropic
> ; Time constant (ps), compressibility (1/bar) and reference P (bar)
> tau_p                    = 0.5
> compressibility          = 4.5e-5
> ref_p                    = 1.0
> ; Random seed for Andersen thermostat
> andersen_seed            = 815131
>
> It  will also disassociate .It is strange.
>
> Can anyone of you tell me what is the reason for that?
>
> Thank you in advance.
>
> Yang
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