[EMAIL PROTECTED] wrote:
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.
OK, so they're (interacting with something else to be) generating a
numerical problem.
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.
After the fact, you could choose to translate any atom of your choice to
a fixed point and the system with it, using (say) VMD. It wouldn't mean
much of anything, apart from probably no longer being a simulation in an
inertial reference frame.
Unless there's a meaningful purpose to seeing such a thing in a test
run, it's really not worth anyone's time. If there is, then explaining
it the first time makes you sound much more like someone with a real
issue, than someone just trying to make something fit some preconception
about pleasant appearance.
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
That's probably fine if grompp doesn't complain - but you can delete all
the position restraints with zero force, since they are doing nothing.
Mark
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