Dear Mark,<br> Thanks for your reply.It cleared my doubts.I have one more doubt.i first tried to just minimize the system ( the same spc model).using amber03 and lennard jones6-12 potential.system was well minimized and got converged.<br>
<br><br><br><br>Now i tried copying the same table6-12.xvg, file from gromax lib to my current directory.<br>1.changed the first adn second parameter to 1 in defaults section in amber03 ff.itp<br>2.since ffnonbonded section is in terms of sigma and epsilon i converted the sigma and epilon columns to A and B (a=4epsi^6 adn b=4epsi8sig^12)<br>
3.now i just included the folling line in em.mdp file<br><br>pme=user<br>vdwtype=user<br>energygroups=SOL<br><br><br>renamed table_6_12.xvg to table.xvg<br>then i grompped it <br><b> grompp -f em.mdp -c saltwater.gro -p topol.top -o em.tpr -maxwarn 3</b><br>
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.2#<br>Generated 2278 of the 2278 non-bonded parameter combinations<br>Generating 1-4 interactions: fudge = 0.5<br>Generated 2278 of the 2278 1-4 parameter combinations<br>
Excluding 2 bonded neighbours molecule type 'SOL'<br>Excluding 2 bonded neighbours molecule type 'SOL'<br>Analysing residue names:<br>There are: 2961 Water residues<br>Number of degrees of freedom in T-Coupling group rest is 26646.00<br>
Largest charge group radii for Van der Waals: 0.039, 0.039 nm<br>Largest charge group radii for Coulomb: 0.084, 0.084 nm<br>This run will generate roughly 5 Mb of data<br><br>Back Off! I just backed up em.tpr to ./#em.tpr.2#<br>
<br>gcq#42: "Out Of Register Space (Ugh)" (Vi)<br><br>then mdrun<br> <b> mdrun -s em.tpr -o em.trr -e em.edr </b><br>Steepest Descents:<br> Tolerance (Fmax) = 1.00000e+03<br> Number of steps = 2000<br>
<br>Reached the maximum number of steps before reaching Fmax < 1000<br><br>writing lowest energy coordinates.<br><br>Back Off! I just backed up confout.gro to ./#confout.gro.2#<br><br>Steepest Descents did not converge to Fmax < 1000 in 2001 steps.<br>
Potential Energy = 1.5031059e+07<br>Maximum force = 3.4432207e+04 on atom 1357<br>Norm of force = 6.4161267e+02<br><br>gcq#197: "I Do It All the Time" (Magnapop)<br><br><br>Now my questions are<br><br>
1. I had experimented with the same potential 6-12 but why didnt the sys didnt get converged when i usethe same orginal potential as user specified potential.?<br>2.are there any other terms to be included apart Fromm table in .mdp file ?<br>
<br><br><br><br><br>added theses lines in topolgy<br><br><div class="gmail_quote">On Wed, May 25, 2011 at 3:21 PM, Mark Abraham <span dir="ltr"><<a href="mailto:mark.abraham@anu.edu.au">mark.abraham@anu.edu.au</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div class="im"><span>On 25/05/11, <b>sreelakshmi ramesh </b> <<a href="mailto:sree.lakshmi@research.iiit.ac.in" target="_blank">sree.lakshmi@research.iiit.ac.in</a>> wrote:</span><blockquote style="border-left: 1px solid rgb(0, 0, 255); padding-left: 13px; margin-left: 0pt;" type="cite">
<div>Hai all,<br> My system is just a water Spc model. <br> I am trying to create a table.xvg which would deal with nonbonded intearction for water-water for say SPC model.<br><br>If i have to calculate the potential i have to consider the interaction between <br>
1.O of water1--O of water 2(LJ+COLOUMB) [CREATED A TABLE that containsr, f (r), −f (r), g(r),−g (r), h(r) and −h (r) ]<br>2.H of water 1--O of water 2(COLOUMB) [ are tables needed ?]<br>3.H of water 1--H of water 2(COLOUMB) [are tables needed ?]</div>
</blockquote><br></div>That depends whether you're trying to apply a different or the same functional form to the interactions of the hydrogen atoms, i.e. whether you have an energy group for the whole system, or have O and H in different energy groups so that you can apply different functional forms to different interactions.<div class="im">
<br> <br><blockquote style="border-left: 1px solid rgb(0, 0, 255); padding-left: 13px; margin-left: 0pt;" type="cite"><div>for 2 and 3rd case should i create 2 tables respectively ? if not how is the potential is calculated for the the last two cases ?</div>
</blockquote><br></div>The user table applies to all interactions unless you start playing around with energygrp_table. So your hydrogen interactions use the table, but only look up the values for f.<div class="im"><br><br>
<blockquote style="border-left: 1px solid rgb(0, 0, 255); padding-left: 13px; margin-left: 0pt;" type="cite"><div>and if it has to be to created since the lennard jones part say g(r),−g (r), h(r) and −h (r) is zero for all values of r should i just create a table with r,f(r)and -f'(r) for last two cases?</div>
</blockquote><br></div>6.7.2 covers this last point.<br><font color="#888888"><div><br>Mark<br>
</div>
</font><br>--<br>
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