<div>Hi all,</div>
<div> </div>
<div>1) added -table tablefile1 -table tablefile2 etc.. to mdrun command ...</div>
<div>2)Increased table-extension parameter from 0.0 to 1.0 and added those values to the table too...</div>
<div> Works now!</div>
<div> </div>
<div>Thanks Mark and ms!</div>
<div> </div>
<div>Pooja<br><br></div>
<div class="gmail_quote">On Tue, Nov 23, 2010 at 7:03 PM, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span> wrote:<br>
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<div class="h5">On 24/11/2010 8:42 AM, Sai Pooja wrote:<br>
<blockquote style="BORDER-LEFT: #ccc 1px solid; MARGIN: 0px 0px 0px 0.8ex; PADDING-LEFT: 1ex" class="gmail_quote">Hi,<br>I run a simulation of a protein in water(tip3p) system using charmm forcefield. I have specified the following energy groups:<br>
Protein SOL and energy group tables Protein SOL SOL SOL. I set Coulombtype to User and VdW to Cut-off. I then generate tables as specified in the manual. To test the validity of these tables, I standard Coulomb and LJ6,12 tables.<br>
I generate 4 tables - table.xvg, table_Protein_SOL.xvg, table_SOL_SOL.xvg and tablep.xvg (all identical)<br>When I run grompp I get no errors. When I run mdrun, it stops after the first step as LINCS fails to converge.<br>
I run the same simulation by changing the Coulombtype to Cut-off and without the tables and it runs.<br>Can you suggest what could be going wrong?<br>(python script)<br>Command used: cmd += '(%s/mdrun_mpi -s rex_%d.tpr -e rex_%d -c after_rex_%d -cpi restart%d -cpo restart%d -cpt 0.1 -append -g rexlog%d -x rextraj%d -table table.xvg table_Protein_SOL.xvg table_SOL_SOL.xvg -tablep tablep.xvg >/dev/null); ' %(GROMPATH,i,i,i,i,i,i,i)<br>
I tried this in two ways -<br>1) specified [ nonbonded_param ] for all Protein atoms and tip3p atoms<br>2) Not specifying them separately<br></blockquote><br></div></div>What does the .log file report about the tables it's read? I don't know how the -table mechanism works, but its conceivable that you need -table file1 -table file2 -table file3.<br>
<font color="#888888"><br>Mark</font>
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