normal mdp update from gromacs 3 to gromacs 4

  • Jian
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13 years 5 months ago #420 by Jian
Hi All,

I am working on Martini Lipid Tutorials ( md.chem.rug.nl/~marrink/MARTINI/Tutorial.html ) by using Gromacs 4. It seems that we need a mdp update (the situation is similar to www.mail-archive.com/gmx-users@gromacs.org/msg19902.html ). I followed the advice on the website and get a new mdout.mdp. Could you please tell me how to update it for Martini work?

Thank you!

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13 years 5 months ago #422 by xavier
Replied by xavier on topic mdp update from gromacs 3 to gromacs 4
Well, actual changes are not needed if I recall correctly! It might have a few warning that you should be able to fix easily.

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11 years 4 months ago #1247 by richor
Replied by richor on topic mdp update from gromacs 3 to gromacs 4
Hi xavier ,
Actually when using version 4.0 and above,a warning is emerge:

Warning:For proper integration of the Berendsen barostat, tau_p (0.5) should be
at least 10 times larger than nstpcouple*dt (0.4)

At this moment,which parameter should I change?

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11 years 4 months ago #1250 by djurre
Replied by djurre on topic mdp update from gromacs 3 to gromacs 4
You have three options:
1) Use -maxwarn 1 and ignore the warning. (This might lead to small integration error's.
2) Lower nstpcouple and dt, so their product becomes <= 0.05.
3) Increase tau_p to 4 or higher.

I would do either 1) or a combination of 2) and 3). Eg. Tau_p = 3.0 and dt = 0.03

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11 years 4 months ago #1252 by richor
Replied by richor on topic mdp update from gromacs 3 to gromacs 4
Thanks!

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