<br><br><div class="gmail_quote">On Fri, May 18, 2012 at 12:20 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div class="HOEnZb"><div class="h5"><br>
<br>
On 5/18/12 6:58 AM, Steven Neumann wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Dear Gmx Users,<br>
<br>
My system consists of a Tube made of Oxygen, Hydrogen and ions. These atoms are<br>
not connected via bonds. I try tu run EM:<br>
<br>
; minim.mdp - used as input into grompp to generate em.tpr<br>
; Parameters describing what to do, when to stop and what to save<br>
<br>
integrator = steep ; Algorithm (steep = steepest descent minimization)<br>
emtol = 1000.0 ; Stop minimization when the maximum force < 1000.0<br>
kJ/mol/nm<br>
emstep = 0.001<br>
nsteps = 50000 ; Maximum number of (minimization) steps to perform<br>
nstxout = 1<br>
; Parameters describing how to find the neighbors of each atom and how to<br>
calculate the interactions<br>
nstlist = 1 ; Frequency to update the neighbor list and long range forces<br>
ns_type = grid ; Method to determine neighbor list (simple, grid)<br>
rlist = 1.4 ; Cut-off for making neighbor list (short range forces)<br>
coulombtype = PME ; Treatment of long range electrostatic interactions<br>
rcoulomb = 1.4 ; Short-range electrostatic cut-off<br>
rvdw = 1.4 ; Short-range Van der Waals cut-off<br>
pbc = xyz ; Periodic Boundary Conditions (yes/no)<br>
<br>
freezegrps = TUB<br>
freezedim = Y Y Y<br>
<br>
<br>
Then a lot of errors "water molecule on atom X cannot be settled". I tried:<br>
<br>
1. constraints = none<br>
<br>
2. remove those water molecules - then other water molecules have the same error<br>
<br>
3. using nstxout =1 in VMD, I could observe that some of the molecules facing<br>
this error split in one frame (hydrogens 7A away from oxygen) or spin around 180<br>
degrees - it depends.<br>
<br>
4. I tried increase vdwradii of the atoms which form my Tube so they wont<br>
overlap with water<br>
<br>
<br>
If you have any suggestions I will really appreciate,<br>
<br>
</blockquote>
<br></div></div>
This is starting to sound more and more like a topology instability. Can you successfully run EM on your tube in the absence of water? If not, then the problem is with the definition of the tube, with the water problems being a consequence.<br>
<br>
-Justin<span class="HOEnZb"><font color="#888888"><br>
<br></font></span></blockquote><div><br>Thank you. I tried without water and it works really fine. However, the posted mdp with water was with the emtol = 1000 - then NO errors occur. When I decrease it to 100 then this error appears. I will try to process it to NVT and see how it goes.<br>
<br> </div><blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><span class="HOEnZb"><font color="#888888">
-- <br>
==============================<u></u>==========<br>
<br>
Justin A. Lemkul, Ph.D.<br>
Research Scientist<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>==========<br>
-- <br>
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</font></span></blockquote></div><br>