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<body class='hmmessage'><div style="text-align: left;">Hi,<br><br>I should remove the warning of cut-off with TPI.<br>It would be nice if you could use PME, but that requires a lot of coding.<br>Note that you should probably use quite a long cut-off.<br><br>The result indeed depends on nsteps, as you should expect.<br>nsteps should be so large that your results converge.<br>But for convergence it is also required that you have enough sampling<br>of your original system in and over all your frames.<br></div><br>Berk<br><br><hr id="EC_stopSpelling">Date: Mon, 3 Nov 2008 22:37:57 +0800<br>From: zgzhangcn@gmail.com<br>To: gmx-users@gromacs.org<br>Subject: [gmx-users] Problems of test particle insertion with gromacs 4.0<br><br><div>Hi all,</div>
<div> I'm trying to use gromacs 4.0 to carried out some calculations with test particle insertion algorithm. </div>
<div> Here are my operations:</div>
<div> 0. Carried out a common NPT simulation with N molecules, I got the .trr file;</div>
<div> 1. prepare .top and .gro with N+1 molecules (including the test particle);<br> 2. use grompp to get the .tpr for mdrun;<br> 3. mdrun -rerun .trr.</div>
<div> In this way, I finally got two files tpi.xvg and tpidist.xvg. The procedure seems fine, isn't it?</div>
<div> Nevertheless, I have some problems here:</div>
<div> 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?</div>
<div> 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?</div>
<div> </div>
<div>Thanks for your possible suggestions!</div>
<div> </div>
<div>zgzhang</div>
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