Dear votca users, I thought I was able to successfully incorporated the tabulated dihedrals in the CG simulation. I could, indeed, simulated for few thousands of steps. But for every run after some time, the simulation stops. I have attached the error file corresponding each runs. I have used the same potentials to generate the tpr file for each run.
I have tried few strategies (listed below) but none of them works.
1. Changed the time step (dt) from 5 fs to 1 fs.
The simulation runs for few thousands of steps and then crashes. It
prints the one of the errors as in the attached file.
2. Played with the extrapolation technique
Quadratic extrapolation : Simulations donot proceed. Exits at step 0
For others techniques (constant, linear, exponential and sasha):
Simulation does proceeds but after thousands of step, one of the error
message is printed.
BTW, when I switch off the dihedrals the simulation executes. It doesnot
crashes.
I have attached the potentials used for the simulations at
https://www.dropbox.com/sh/hdudrulbmgfu3q6/Dsb9XTnnRp.
The potentials were extrapolated using the linear method.
I have no clue what else could cause the problem. Any insight upon this
would be very helpful.
Chandan
--
Chandan kumar Choudhury
NCL, Pune
INDIA
On Wed, Oct 30, 2013 at 6:37 PM, Chandan Choudhury <[email protected]>wrote:
> Thanks Christoph. Your responses are very fruitful.
>
> Finally, I am able to incorporated the tabulated dihedrals for CG
> simulations.
>
> On a side note: One be very cautious while dealing with the tab. pot. For
> dihedrals, I used linear function to extrapolate the smoothed potentials.
> And of-course, always use whole (pbc whole) configurations.
>
>
> Chandan
>
>
> --
> Chandan kumar Choudhury
> NCL, Pune
> INDIA
>
>
> On Fri, Oct 18, 2013 at 4:46 AM, Christoph Junghans <[email protected]>wrote:
>
>> 2013/10/14 Chandan Choudhury <[email protected]>:
>> >
>> > Dear votca users,
>> >
>> > I intend to use the dihedral tabulated potentials. I have generated the
>> > distributions and potentials from csg_boltzmann. Then I use the
>> following
>> > commands to generate the tab. potentials.
>> >
>> > Here smoothing is necessary as the potential is noisy. I use the
>> quadratic
>> > extrapolation.
>> >
>> > source /opt/apps/gmx/single/463/bin/GMXRC
>> > GMXLIB=/opt/apps/gmx/single/463/share/gromacs/top
>> > source /opt/apps/votca/1.2.3/bin/VOTCARC.bash
>> >
>> > sed -e '1,2d' -e 's/$/ i/' $1.dihedral.pot | tac | sed -e '1,1d' | tac >
>> > $1.dihedral.cut
>> > csg_call table smooth $1.dihedral.cut $1.dihedral.smooth
>> > csg_resample --in $1.dihedral.smooth --out $1.dihedral.refined --grid
>> > -3.141::0.001:3.141
>> > csg_call table extrapolate --function quadratic $1.dihedral.refined
>> > $1.dihedral.ep
>> > awk '{print $1/3.141592654*180.0,$2}' $1.dihedral.ep >
>> $1.dihedral.pot.cur
>> > csg_call --ia-type dihedral --ia-name $1.dihedral --options convert.xml
>> > convert_potential gromacs
>> >
>> > The tabulated potentials are used for the dihedrals. On using these
>> > potentials, I get the errors (Please see attached log file). These error
>> > also pops when I use -nt=1.
>> >
>> > When I fit a RB potential function to the dihedrals (smoothed
>> potential) and
>> > use the function type 3 for it, the simulation proceeds.
>> > Also, when I switch off the dihedrals (by commenting the topol.top), the
>> > simulation executes without any problem.
>> >
>> > I have also attached the topology and the structure file for the
>> reference.
>> >
>> > Does anyone has encounter this type of problem. Is there some way to
>> tackle
>> > dihedrals. Any insight would be very fruitful.
>> Either your table isn't long enough or the system is exploding in the 1st
>> step.
>> Make sure your conf.gro has correct pbc, running trjconv -pbc mol might
>> help.
>> Or try to minimize with some harmonic potentials first.
>>
>> Cheers,
>>
>> Christoph
>>
>> >
>> > Chandan
>> >
>> > --
>> > Chandan kumar Choudhury
>> > NCL, Pune
>> > INDIA
>> >
>> > --
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>>
>>
>>
>> --
>> Christoph Junghans
>> Web: http://www.compphys.de
>>
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>
>
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dih_error
Description: Binary data
