[gmx-users] position restraints
gadies at fh.huji.ac.il
gadies at fh.huji.ac.il
Thu Apr 24 14:49:56 CEST 2008
Hi,
I minimized without restraints, could that be the problem?
After the minimization I got a Potential Energy = -6.1434351e+02.
Gadi
Quoting "Justin A. Lemkul" <jalemkul at vt.edu>:
> Quoting gadies at fh.huji.ac.il:
>
>> 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
>
> Basic information about this type of error can be found here (as
> well as several
> hundred posts in the list archive):
>
> http://wiki.gromacs.org/index.php/Errors#LINCS_warnings
>
> How did you do your minimization, with or without restraints? Did
> it converge
> to an acceptable potential energy?
>
> -Justin
>
>>
>> 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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>>
>>
>>
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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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