[gmx-users] position restraints
gadies at fh.huji.ac.il
gadies at fh.huji.ac.il
Thu Apr 24 13:34:03 CEST 2008
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" <jalemkul at vt.edu>:
>
> 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 gadies at fh.huji.ac.il:
>
>>
>> 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 <Mark.Abraham at anu.edu.au>:
>>
>> > gadies at fh.huji.ac.il 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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>>
>>
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>
>
>
> ========================================
>
> Justin A. Lemkul
> Graduate Research Assistant
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul at vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/
>
> ========================================
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