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