<div>Hi,</div><div><br></div><div>I am getting these notes when I run grompp:</div><div><br></div><div>NOTE 3 [file Init/ffsb_init.top]:</div><div> The largest charge group contains 12 atoms.</div><div> Since atoms only see each other when the centers of geometry of the charge</div>
<div> groups they belong to are within the cut-off distance, too large charge</div><div> groups can lead to serious cut-off artifacts.</div><div> For efficiency and accuracy, charge group should consist of a few atoms.</div>
<div> For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc.</div><div><br></div><div>initialising group options...</div><div>processing index file...</div><div>Analysing residue names:</div><div>There are: 3484 OTHER residues</div>
<div>There are: 67 PROTEIN residues</div><div>There are: 0 DNA residues</div><div>There are: 0 RNA residues</div><div>Analysing Protein...</div><div>Analysing Other...</div><div>Making dummy/rest group for Acceleration containing 11343 elements</div>
<div>Making dummy/rest group for Freeze containing 11343 elements</div><div>Making dummy/rest group for VCM containing 11343 elements</div><div>Number of degrees of freedom in T-Coupling group Protein is 1777.76</div><div>
Number of degrees of freedom in T-Coupling group non-Protein is 20898.23</div><div>Making dummy/rest group for User1 containing 11343 elements</div><div>Making dummy/rest group for User2 containing 11343 elements</div><div>
Making dummy/rest group for XTC containing 10450 elements</div><div>Making dummy/rest group for Or. Res. Fit containing 11343 elements</div><div>Making dummy/rest group for QMMM containing 11343 elements</div><div>T-Coupling has 2 element(s): Protein non-Protein</div>
<div>Energy Mon. has 2 element(s): Protein non-Protein</div><div>Acceleration has 1 element(s): rest</div><div>Freeze has 1 element(s): rest</div><div>User1 has 1 element(s): rest</div><div>User2 has 1 element(s): rest</div>
<div>VCM has 1 element(s): rest</div><div>XTC has 2 element(s): Protein rest</div><div>Or. Res. Fit has 1 element(s): rest</div><div>QMMM has 1 element(s): rest</div><div>Checking consistency between energy and charge groups...</div>
<div>Largest charge group radii for Van der Waals: 0.288, 0.263 nm</div><div>Largest charge group radii for Coulomb: 0.288, 0.263 nm</div><div><br></div><div>NOTE 4 [file nvtp.mdp]:</div><div> The sum of the two largest charge group radii (0.551009) is larger than</div>
<div> rlist (2.000000) - rvdw (2.000000)</div><div><br></div><div>Can someone tell me how to correct these?</div><div><br></div>Pooja<br><div class="gmail_quote">On Thu, Jul 15, 2010 at 7:06 PM, Sai Pooja <span dir="ltr"><<a href="mailto:saipooja@gmail.com">saipooja@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><div>Hi,</div><div><br></div><div>NOTE 4 [file /fs/home/sm868/llamapooja/ffsb/Setup/nvt.mdp]:</div><div> The sum of the two largest charge group radii (0.510406) is larger than</div>
<div> rlist (2.000000) - rvdw (2.000000)</div>
<div><br></div><div><br></div><div><br></div><div>NOTE 5 [file /fs/home/sm868/llamapooja/ffsb/Setup/nvt.mdp]:</div><div> The sum of the two largest charge group radii (0.510406) is larger than</div><div> rlist (2.000000) - rcoulomb (1.800000)</div>
<div><br></div><div>How does this effect the simulation? Do these introduce errors?</div><div><br></div><div>Pooja</div><br><font color="#888888">-- <br>Quaerendo Invenietis-Seek and you shall discover.<br>
</font></blockquote></div><br><br clear="all"><br>-- <br>Quaerendo Invenietis-Seek and you shall discover.<br>