It seems that I've fixed that problem by reduce vdv radii for Cl during defining of my box<br><br>Eventually I've obtained box with the desired density<br> than I've delete vdvradii.dat for my wor dir<br><br>by when I've launched equilibration I've oibtained<br>
<br>Fatal error:<br>Too many LINCS warnings (1598)<br>If you know what you are doing you can adjust the lincs warning threshold in your mdp file<br><br>I've never seen this before<br><br>I'm using 1.o cutoff for pme and 1.4 for vdv<br>
my LINKS parameters are<br><br>; Bond parameters<br>continuation = no ; first dynamics run<br>constraint_algorithm = lincs ; holonomic constraints <br>constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained<br>
lincs_iter = 1 ; accuracy of LINCS<br>lincs_order = 4 ; also related to accuracy<br><br>How I could solve it?<br><br><br>James<br><br><div class="gmail_quote">2012/2/14 James Starlight <span dir="ltr"><<a href="mailto:jmsstarlight@gmail.com">jmsstarlight@gmail.com</a>></span><br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Mark,<br><br>I've checked only density value<br><br>with 500 molecules Ccl4 I have density that is twisely less that I need ( in accordance to the literature ). Also I've checked my box visually and found that the box is not properly tightly packed so I dont know why genbox didnt add some extra mollecules :(<br>
<br>In other words I wounder to know if there is any way to add some extra molecules to the pre defined box to make my system more tighly packed ( to short distance between existing molecules and place new ones in the new space ) ?<span class="HOEnZb"><font color="#888888"><br>
<br>James</font></span><div class="HOEnZb"><div class="h5"><br><br><div class="gmail_quote">2012/2/14 Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>></span><br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div>On 14/02/2012 4:57 PM, James Starlight wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Justin,<br>
<br>
Firstly I've created the box of desired size with only 500 molecules ( I need 1000)<br>
<br>
Than I've tried to add extra 200 molecules by means of Genbox<br>
<br>
genbox -cp super_box.gro -ci Ccl4.gro -nmol 200 -o new_solv.gro<br>
<br>
but no molecules have been added<br>
Added 0 molecules (out of 200 requested) of Cl4<br>
</blockquote>
<br></div>
... then there are no gaps large enough to insert your molecules. Either make gaps, or check out genbox -h for advice on defining the radii.<div><br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
also I've tried<br>
<br>
genbox -cp super_box.gro -cp Ccl4.gro -nmol 200 -o new_solv.gro<br>
</blockquote>
<br></div>
Two -cp options is not what you want, and -nmol probably only works with -ci.<div><br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
but system were crashed with message<br>
<br>
Reading solute configuration<br>
God Rules Over Mankind, Animals, Cosmos and Such<br>
Containing 2500 atoms in 500 residues<br>
Initialising van der waals distances...<br>
<br>
WARNING: masses and atomic (Van der Waals) radii will be determined<br>
based on residue and atom names. These numbers can deviate<br>
from the correct mass and radius of the atom type.<br>
<br>
Reading solvent configuration<br>
"God Rules Over Mankind, Animals, Cosmos and Such"<br>
solvent configuration contains 5 atoms in 1 residues<br>
<br>
<br>
Is there any ways to add extra mollecules to the pre defined box ?<br>
</blockquote>
<br></div>
Yes - but there has to be room for them.<span><font color="#888888"><br>
<br>
Mark</font></span><div><div><br>
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