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<div>Hi,</div>
<div>Thanks a lot, Tsjerk ! My simulation is running.</div>
<div>I never knew that a discrepancy between the the .top file and .gro, grompp uses the topology information in stead of<br>the coordinate file information.</div>
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<div>What does issue a set of warnings by grompp ?</div>
<div>How do you know the discrepancy between the the .top file and .gro will make simulation wrong?</div>
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<div>Thank you</div>
<div>Lin</div>
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<div>Hi,</div>
<div>> Tsjerk gave me suggestion to check the .tpr file created by the command<br>> grompp.</div>
<div>I also suggested to try and find out why the water molecules got garbled.</div>
<div>Between adding solvent and energy minimization, you also added<br>chloride to counter the net positive charge. I assume you used genion<br>for that, which is the most sensible way to do so. Genion typically<br>adds the ions at the end of the topology. I further assume that you<br>
manually updated the topology by adding a line 'CL- 26' under [<br>system ]. But if you inserted that line _before_ the line specifying<br>the number of solvent molecules, whereas in your .gro the chloride<br>ions were at the end of it, then you had a discrepancy between the<br>
two. In such cases, grompp uses the topology information in stead of<br>the coordinate file information, but does issue a set of warnings. If<br>my assumptions are correct, then if you had sent the grompp output at<br>first instance, we would have been immediately able to pinpoint your<br>
error. Besides, if you had looked at the output from grompp yourself,<br>you would (should) have noticed that something was wrong there.</div>
<div>Cheers,</div>
<div>Tsjerk</div>
<div><br>--<br>Tsjerk A. Wassenaar, Ph.D.</div>
<div>Computational Chemist<br>Medicinal Chemist<br>Neuropharmacologist</div>