no prob you wait for some time it will write topology file and the proceed further..<br><br><div class="gmail_quote">On Thu, Apr 24, 2008 at 5:04 PM, <<a href="mailto:gadies@fh.huji.ac.il">gadies@fh.huji.ac.il</a>> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">Hi,<br>
<br>
The full mdrun output when the simulation blows up is:<br>
<br>
Step 0, time 0 (ps) LINCS WARNING<br>
relative constraint deviation after LINCS:<br>
max inf (between atoms 6 and 7) rms inf<br>
bonds that rotated more than 30 degrees:<br>
.<br>
.<br>
.<br>
Warning: 1-4 interaction between 1 and 6 at distance 324490777485109120.000 which is larger than the 1-4 table size 1.000 nm<br>
These are ignored for the rest of the simulation<br>
This usually means your system is exploding,<br>
if not, you should increase table-extension in your mdp file<br>
<br>
Thanks Gadi<br>
<br>
Quoting "Justin A. Lemkul" <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>:<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<br>
Did your minimization converge to a nice, negative potential energy? Also, what<br>
is the full mdrun output when the simulation blows up? You've quoted the last<br>
bit, but it would be more informative to see the whole output, or at least a<br>
description of it (i.e., LINCS warnings).<br>
<br>
-Justin<br>
<br>
Quoting <a href="mailto:gadies@fh.huji.ac.il" target="_blank">gadies@fh.huji.ac.il</a>:<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<br>
Hi,<br>
<br>
I tried using no temperature coupling and no constraints, that did not help.<br>
If I run the simulation without the position restraints it works OK.<br>
Could there by something wrong with the posre file (I'll attach it at<br>
the end of the email).<br>
I want one of the atoms in the lipid to stay in one place and the rest<br>
to wiggle around it. Is there any other way to do that which is not<br>
position restraints.<br>
<br>
Thanks Gadi<br>
<br>
<br>
[ position_restraints ]<br>
; atom type fx fy fz<br>
1 1 0 0 0<br>
2 1 0 0 0<br>
3 1 0 0 0<br>
4 1 0 0 0<br>
5 1 0 0 0<br>
6 1 0 0 0<br>
7 1 0 0 0<br>
8 1 1000.0 1000.0 1000.0<br>
9 1 0 0 0<br>
10 1 0 0 0<br>
11 1 0 0 0<br>
12 1 0 0 0<br>
13 1 0 0 0<br>
14 1 0 0 0<br>
15 1 0 0 0<br>
16 1 0 0 0<br>
17 1 0 0 0<br>
18 1 0 0 0<br>
19 1 0 0 0<br>
20 1 0 0 0<br>
21 1 0 0 0<br>
22 1 0 0 0<br>
23 1 0 0 0<br>
24 1 0 0 0<br>
25 1 0 0 0<br>
26 1 0 0 0<br>
27 1 0 0 0<br>
28 1 0 0 0<br>
29 1 0 0 0<br>
30 1 0 0 0<br>
31 1 0 0 0<br>
32 1 0 0 0<br>
33 1 0 0 0<br>
34 1 0 0 0<br>
35 1 0 0 0<br>
36 1 0 0 0<br>
37 1 0 0 0<br>
38 1 0 0 0<br>
39 1 0 0 0<br>
40 1 0 0 0<br>
41 1 0 0 0<br>
42 1 0 0 0<br>
43 1 0 0 0<br>
44 1 0 0 0<br>
45 1 0 0 0<br>
46 1 0 0 0<br>
47 1 0 0 0<br>
48 1 0 0 0<br>
49 1 0 0 0<br>
50 1 0 0 0<br>
<br>
Quoting Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>>:<br>
<br>
> <a href="mailto:gadies@fh.huji.ac.il" target="_blank">gadies@fh.huji.ac.il</a> wrote:<br>
><br>
> Please generate replies to the mailing list sensibly. It's very hard to<br>
> work out who you are quoting where in this email. It'd be easy just to<br>
> ignore it, and that's the last thing you should want.<br>
><br>
>> Hello,<br>
>><br>
>> I'm trying to run a simulation with one lipid molecule in a fixed<br>
>> simulation box without pbc.<br>
>> I set position restraints on one of the atoms and I seem to keep on<br>
>> getting the following error:<br>
><br>
> Why do you want MD of a single lipid and a position restraint on one<br>
> atom? If you just want to see a lipid wiggle around, then don't create<br>
> more numerical complexity.<br>
><br>
>> The lipid is DPPC.The .itp file I got from a coworker that used it<br>
>> before for membrane MD simulations.<br>
>> To minimize the system I used steepest descent with the following<br>
>> parameters:<br>
><br>
> Well if your grompp and mdrun completed successfully and without<br>
> warnings then you've probably got an OK topology and structure.<br>
><br>
> The combination of all bond constraints, a single lipid in vacuo,<br>
> temperature coupling and a single position restraint sounds like a<br>
> recipe for a numerical disaster, i.e. blowing up. Try with fewer of<br>
> those things applied, or get a more physically-reasonable system, like<br>
> a whole membrane.<br>
><br>
> Mark<br>
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<br>
<br>
========================================<br>
<br>
Justin A. Lemkul<br>
Graduate Research Assistant<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> | (540) 231-9080<br>
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