[gmx-users] simulation using tabulated dihedral potentials.
Chandan Choudhury
iitdckc at gmail.com
Tue Dec 10 10:48:15 CET 2013
On Mon, Dec 9, 2013 at 8:20 PM, Chandan Choudhury <iitdckc at gmail.com> wrote:
>
>
> On Mon, Dec 9, 2013 at 6:46 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 12/9/13 8:09 AM, Chandan Choudhury wrote:
>>
>>> On Mon, Dec 9, 2013 at 5:41 PM, Mark Abraham <mark.j.abraham at gmail.com>
>>> wrote:
>>>
>>> Do your tabulated functions work on a toy system, like butane?
>>>>
>>>> No Mark. I didnot try with butane. The simulation stops when I
>>> incorporated
>>> tabulated dihedral potential.
>>>
>>>
>> Which is precisely why Mark is suggesting that you test something simple.
>> If the simulation runs using a normal potential, but fails with your
>> tabulated potential, that suggests quite strongly that your tabulated
>> potential is not sound. So you need to go back to something very simple
>> that should have a very obvious outcome and scrutinize its success or
>> failure, then move on to something slightly more complex, etc until it
>> fails and you identify where the problem lies.
>>
>
> Thanks for the reply.
>
> Initially the system had 80 chains. Now I reduced it to single chain. The
> single chains consisted of just 12 Coarse Grained beads.
> The simulation proceeds very smoothly for 200000000 steps.
> The tabulated bond, tab. angle and tab. dihedral potentials were on.
>
> Few more updates.
I now increased the no. of chains to 10. The system now consists of 120
beads. Will all the tabulated potentials, following is the snippet form the
log file:
Step Time Lambda
77670000 388350.00000 0.00000
Energies (kJ/mol)
Tab. Bonds Tab. Angles Tab. Dih. LJ (SR) Coulomb (SR)
2.03886e+02 5.00884e+02 1.33715e+02 9.77543e+01 0.00000e+00
Potential Kinetic En. Total Energy Temperature Pressure (bar)
9.36239e+02 7.78233e+02 1.71447e+03 5.24366e+02 6.92929e+01
Step Time Lambda
77675000 388375.00000 0.00000
Energies (kJ/mol)
Tab. Bonds Tab. Angles Tab. Dih. LJ (SR) Coulomb (SR)
nan 3.50433e+06 nan 0.00000e+00 0.00000e+00
Potential Kinetic En. Total Energy Temperature Pressure (bar)
nan -nan -nan -nan -nan
Step Time Lambda
77680000 388400.00000 0.00000
Energies (kJ/mol)
Tab. Bonds Tab. Angles Tab. Dih. LJ (SR) Coulomb (SR)
nan 3.50433e+06 nan 0.00000e+00 0.00000e+00
Potential Kinetic En. Total Energy Temperature Pressure (bar)
nan -nan -nan -nan -nan
Step Time Lambda
77685000 388425.00000 0.00000
Energies (kJ/mol)
Tab. Bonds Tab. Angles Tab. Dih. LJ (SR) Coulomb (SR)
nan 3.50433e+06 nan 0.00000e+00 0.00000e+00
Potential Kinetic En. Total Energy Temperature Pressure (bar)
nan -nan -nan -nan -nan
........
........
Writing checkpoint, step 200000000 at Tue Dec 10 00:12:21 2013
Energies (kJ/mol)
Tab. Bonds Tab. Angles Tab. Dih. LJ (SR) Coulomb (SR)
nan 3.50433e+06 nan 0.00000e+00 0.00000e+00
Potential Kinetic En. Total Energy Temperature Pressure (bar)
nan -nan -nan -nan -nan
<====== ############### ==>
<==== A V E R A G E S ====>
<== ############### ======>
Statistics over 200000001 steps using 2000001 frames
Energies (kJ/mol)
Tab. Bonds Tab. Angles Tab. Dih. LJ (SR) Coulomb (SR)
nan 2.14355e+06 nan 3.19828e+01 0.00000e+00
Potential Kinetic En. Total Energy Temperature Pressure (bar)
nan -nan -nan -nan -nan
Total Virial (kJ/mol)
-nan -nan -nan
-nan -nan -nan
-nan -nan -nan
Pressure (bar)
-nan -nan -nan
-nan -nan -nan
-nan -nan -nan
Due the limitation in the no. of beads, the simulation runs on single
processor. The mdrun doesnot show any error. It proceeds upto 200000000
steps. But we can see from the log file after 77675000 steps there is some
problem.
I also run a simulation with just 2 chains (24 beads). The simulation
proceeds smoothly. Output of log file:
199995000 999975.00000 0.00000
Energies (kJ/mol)
Tab. Bonds Tab. Angles Tab. Dih. LJ (SR) Coulomb (SR)
2.01529e+01 8.50365e+01 1.34663e+01 1.44338e+00 0.00000e+00
Potential Kinetic En. Total Energy Temperature Pressure (bar)
1.20099e+02 1.92775e+02 3.12874e+02 6.72038e+02 2.80949e+01
Step Time Lambda
200000000 1000000.00000 0.00000
Writing checkpoint, step 200000000 at Tue Dec 10 15:10:21 2013
Energies (kJ/mol)
Tab. Bonds Tab. Angles Tab. Dih. LJ (SR) Coulomb (SR)
2.50423e+01 1.12245e+02 1.85350e+01 2.55573e+00 0.00000e+00
Potential Kinetic En. Total Energy Temperature Pressure (bar)
1.58378e+02 1.69571e+02 3.27949e+02 5.91148e+02 6.65343e+00
<====== ############### ==>
<==== A V E R A G E S ====>
<== ############### ======>
Statistics over 200000001 steps using 2000001 frames
Energies (kJ/mol)
Tab. Bonds Tab. Angles Tab. Dih. LJ (SR) Coulomb (SR)
4.48786e+01 8.97012e+01 2.00644e+01 2.34681e+00 0.00000e+00
Potential Kinetic En. Total Energy Temperature Pressure (bar)
1.56991e+02 1.44750e+02 3.01741e+02 5.04619e+02 1.54418e+00
Total Virial (kJ/mol)
4.35571e+01 8.71257e-02 2.84028e-01
8.71252e-02 4.38582e+01 3.08832e-01
2.84028e-01 3.08832e-01 4.37737e+01
Pressure (bar)
1.60808e+00 -2.94158e-02 -7.80104e-02
-2.94156e-02 1.48653e+00 -1.01639e-01
-7.80103e-02 -1.01639e-01 1.53793e+00
I donot understand what might be the problem. Is it actually the input
tabulated potentials or something else?
Some insight to it would be very helpful.
Chandan
> Chandan
>
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 601
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>>
>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>>
>> ==================================================
>>
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