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?
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
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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