Dear Justin,<br><br>Thanks for your reply. You said "....You should avoid ad hoc changes."<br>You used different parameters for energy minimization at tutorial called "Tutorial 5: Protein-Ligand Complex".<br>
<u><b>a part of your em.mdp</b></u><br>nstlist = 1 <br>rlist = 1.0 <br>rcoulomb = 1.0<br>rvdw = 1.0 <br><u><b>a part of your md.mdp</b></u><br>nstlist = 5 <br>rlist = 0.9 <br>rcoulomb = 0.9 <br>rvdw = 1.4<br>
<br>Then, <span id="result_box" class="short_text" lang="en"><span class="hps">Why did</span> <span class="hps">you change </span><span class="hps">some parameters</span></span> (nstlist,rlist,rcoulomb,rvdw) for energy minimization? <br>
<br>Thanks in advance<br><br><div class="gmail_quote">23 Mart 2012 19:31 tarihinde Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> yazdı:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div class="im"><br>
<br>
ahmet yıldırım wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Dear users,<br>
<br>
I am using the Reaction-Field method for electrostatics interactions. I used the following parameters for all input files (em.mdp, pr.mdp, nvt.mdp, npt.mdp, md.mdp). I just changed as an epsilon_rf=78 in md.mdp. If I set nstlist=rlist=rcoulomb=rvdw=1.<u></u>0 for energy minimization, would not it be better? What is your suggestions?<br>
<br>
</blockquote>
<br></div>
Why do you think making such changes to the cutoffs would be better? These settings, for the most part, are a fixed part of the force field you're using. Unless you have proof (either by your own demonstration or one that is published) that making such changes result in better results, you should avoid ad hoc changes.<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div class="im">
; Neighbor Searching Parameters<br>
nstlist = 5 ns-type = Grid pbc = xyz rlist = 0.9 ; Electrostatics<br>
coulombtype = Reaction-Field rcoulomb = 1.4 epsilon_rf = 54 ; VdW<br></div>
vdw-type = Cut-off rvdw = 1.4 *<br>
Another question:* I used 200 K (in pr.mdp) and 300 K (in nvt.mdp, npt.mdp and md.mdp) the reference temperature for coupling. I analysed the temperature after production run. I get "Temperature=312.646" (g_energy -f md.edr -o temperature.xvg). that is, The temperature has increased (approximately 12 K) during the simulation. What could be the reason for the increase in temperature? I had setted to 200 K the reference temperature for coupling in pr.mdp. it can cause?<br>
<br>
</blockquote>
<br>
This outcome is precisely what you would expect, simply because you're using the reaction field method and it introduces cutoff artifacts. Interestingly, this same outcome (an increase of exactly 12K) has been reported before:<br>
<br>
<a href="http://lists.gromacs.org/pipermail/gmx-users/2009-January/039113.html" target="_blank">http://lists.gromacs.org/<u></u>pipermail/gmx-users/2009-<u></u>January/039113.html</a><br>
<br>
-Justin<br>
<br>
-- <br>
==============================<u></u>==========<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | <a href="tel:%28540%29%20231-9080" value="+15402319080" target="_blank">(540) 231-9080</a><br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.<u></u>vt.edu/Pages/Personal/justin</a><br>
<br>
==============================<u></u>==========<span class="HOEnZb"><font color="#888888"><br>
-- <br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/<u></u>mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/<u></u>Support/Mailing_Lists/Search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/<u></u>Support/Mailing_Lists</a><br>
</font></span></blockquote></div><br><br clear="all"><br>-- <br>Ahmet Yıldırım<br><br>