[gmx-users] g_energy

Payman Pirzadeh ppirzade at ucalgary.ca
Fri Mar 30 08:07:04 CEST 2012

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? 


-----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 A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080

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