[gmx-users] Problems of test particle insertion with gromacs 4.0

Berk Hess gmx3 at hotmail.com
Mon Nov 3 17:01:16 CET 2008


I should remove the warning of cut-off with TPI.
It would be nice if you could use PME, but that requires a lot of coding.
Note that you should probably use quite a long cut-off.

The result indeed depends on nsteps, as you should expect.
nsteps should be so large that your results converge.
But for convergence it is also required that you have enough sampling
of your original system in and over all your frames.


Date: Mon, 3 Nov 2008 22:37:57 +0800
From: zgzhangcn at gmail.com
To: gmx-users at gromacs.org
Subject: [gmx-users] Problems of test particle insertion with gromacs 4.0

Hi all,
   I'm trying to use gromacs 4.0 to carried out some calculations with test particle insertion algorithm. 
   Here are my operations:
   0. Carried out a common NPT simulation with N molecules, I got the .trr file;
   1. prepare .top and .gro with N+1 molecules (including the test particle);
   2. use grompp to get the .tpr for mdrun;
   3. mdrun -rerun .trr.
   In this way, I finally got two files tpi.xvg and tpidist.xvg. The procedure seems fine, isn't it?
   Nevertheless, I have some problems here:
   1. when I was trying to use pme (or EWALD) for the electrostatics, the grompp stopped with an error: "TPI does not work with full electrostatics". But if I use cut-off, the grompp works but generates a warning to recommend the use of pme or reaction field. What's wrong here?

   2. The final output of mu seems to be sensitive to the choice of nsteps (I've tried from 1000 to 10000). How to choose an appropriate one?
Thanks for your possible suggestions!

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