Re: [gmx-users] simulation settings

[Mark Abraham]

On 1/03/2010 12:00 AM, pol...@fh.huji.ac.il wrote:

Dear Gromacs users and developers,
I want to perform simulation of peptide dissolved in water using NPT.
For constant temperature I use Berendsen temperature coupling. Do I have
to define tc-grps for 2 groups (protein and solvent) or I may use
tc-grps =System.
What is the difference? The person who introduced gromacs to me uses
tc-grps = Protein Sol_Ions
but he is not sure why it should be in this way if at all
Can you, please elucidate this issue to me.


There's some quick advice here 
http://www.gromacs.org/Documentation/Terminology/Thermostats, otherwise 
consult some textbook material.


Mark
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[gmx-users] simulation settings

[politr]

Dear Gromacs users and developers,
I want to perform simulation of peptide dissolved in water using NPT.  
For constant temperature I use Berendsen temperature coupling. Do I  
have to define tc-grps for 2 groups (protein and solvent) or I may use  
tc-grps =System.

What is the difference? The person who introduced gromacs to me uses
tc-grps =  Protein  Sol_Ions
but he is not sure why it should be in this way if at all
Can you, please elucidate this issue to me.
Thank you a lot.
Regina


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