[gmx-users] g_energy

[Payman Pirzadeh]

Hello,
I am using gromacs 4.5.4. In g_energy I see an option about #surf*surfTen.
Could you please clarify how it is calculated? In a system with a protein
and water, what does it correspond to? 
Best,

Paymon

-----Original Message-----
From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
On Behalf Of Justin A. Lemkul
Sent: March-29-12 7:23 PM
To: Acoot Brett; Discussion list for GROMACS users
Subject: Re: [gmx-users] protein melting experiment by GROMACS



Acoot Brett wrote:
> Dear All,
>  
> I remember before I have read a something on melting the protein from 
> a predefined starting temperature to a predefined end temperature by 
> MD, so that after the MD we can look at the whole process to see which 
> part of the protein unfold earlier, which part of the protein of the 
> protein unfold earlier. No I cannot find that introduction.
>  
> After we equilibriate the protein system, will you please tell me how 
> to define the temperature gradient from the start temperature to the 
> end temperature in the mdp file? Or do you have a protocol on it?
>  

See the manual regarding simulated annealing.

-Justin

--
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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