[gmx-users] Different temperature

Andrea Carotti and.carotti at farmchim.uniba.it
Thu Dec 22 17:19:40 CET 2005

I've followed  the procedure of a paper that used gromacs for the MD 
simulation on the same target I have (same xray starting structure). I have 
followed the lines you mentioned:
1) energy minimization to relieve bad contacts after solvation, followed by
2) position-restrained NPT simulations
Do you have some suggestions? do I have to change something or this 
temperature can be considered acceptable?
In other simulations I have found a good reproducibility of some published 
----- Original Message ----- 
From: "Mark Abraham" <Mark.Abraham at anu.edu.au>
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Sent: Thursday, December 22, 2005 4:45 PM
Subject: Re: [gmx-users] Different temperature

> Andrea Carotti wrote:
>> Hi all,
>> sorry for the long message.
>> I'm performing an MD on a system made by a protein and water. I use the 
>> gromos96 ff.
> <snip>
>> As you can see the temperature increase rapidly to a value near 350K. 
>> Could you please explain me the problem (if it's a problem) and point me 
>> out some suggestions to solve it?
> What did you do to the system before this?
> Ordinarily something along the lines of
> 1) energy minimization to relieve bad contacts after solvation, followed 
> by
> 2) (optionally position-restrained) NVT simulation(s) to equilibrate 
> temperatures, followed by
> 3) (optionally position-restrained) NPT simulation(s) to equilibrate P 
> while T is already pretty good
> leads to sensibly equilibrated systems, but your mileage will vary with 
> your system, of course.
> Find some recent MD papers you think relevant/analogous to your system and 
> copy them, if you think they did something reasonable here.
> Mark
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