Dear GMX users,
After I edit vdwradii.dat and run genbox, my program still crashes when
I run position restrained MD with heating the system from 100K to 300K.
When I check the log file. I find the kinetic energy doubles (step 38880
compare to step 38870, by the way, the re_t is the same in these two
steps) when the constraint problem starts to take place. Does anyone
know why KE doubles?
The following message is from my log file:
Step Time Lambda
38870 77.74001 0.00000
Rel. Constraint Deviation: Max between atoms RMS
Before LINCS 0.029985 1381 1382 0.004488
After LINCS 0.002836 360 390 0.002298
Current ref_t for group Protein: 269.4
Current ref_t for group SOL: 269.4
Energies (kJ/mol)
Angle G96Angle Ryckaert-Bell. LJ-14
Coulomb-14
1.86369e+03 8.21120e+02 3.90504e+03 9.13784e+04 1.63718e
+03
LJ (SR) Coulomb (SR) Position Rest. Potential Kinetic
En.
2.63152e+04 -2.08977e+05 1.31793e+03 -8.17386e+04 3.00352e
+04
Total Energy Temperature Pressure (bar)
-5.17034e+04 2.67248e+02 1.12117e+02
Step Time Lambda
38880 77.76000 0.00000
Rel. Constraint Deviation: Max between atoms RMS
Before LINCS 8.028940 1182 1184 0.184534
After LINCS 6.697157 1182 1184 0.153625
Step 38880, time 77.76 (ps) LINCS WARNING
relative constraint deviation after LINCS:
max 6.697157 (between atoms 1182 and 1184) rms 0.153625
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
1182 1184 90.0 0.1090 0.8390 0.1090
1182 1185 50.4 0.1090 0.1093 0.1090
Constraint error in algorithm Lincs at step 38880
Current ref_t for group Protein: 269.4
Current ref_t for group SOL: 269.4
Energies (kJ/mol)
Angle G96Angle Ryckaert-Bell. LJ-14
Coulomb-14
1.92677e+03 8.35797e+02 3.89187e+03 9.12880e+04 1.63733e
+03
LJ (SR) Coulomb (SR) Position Rest. Potential Kinetic
En.
3.17595e+04 -2.09746e+05 1.31354e+03 -7.70932e+04 8.35900e
+04
Total Energy Temperature Pressure (bar)
6.49684e+03 7.43768e+02 4.87090e+03
Step 38881, time 77.762 (ps) LINCS WARNING
relative constraint deviation after LINCS:
max 0.385035 (between atoms 1182 and 1184) rms 0.009398
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
1182 1183 35.1 0.1078 0.1122 0.1090
1182 1184 89.9 0.8390 0.1510 0.1090
1182 1185 57.3 0.1093 0.1129 0.1090
1242 1245 61.1 0.1090 0.1092 0.1090
Thank you for your help!
Dongsheng
On Tue, 2006-07-04 at 09:52 -0400, Dongsheng Zhang wrote:
> mark,
>
> That is a good idea. Thank you very much!
>
>
> Dongsheng
>
>
> On Tue, 2006-07-04 at 15:38 +1000, Mark Abraham wrote:
> > Dongsheng Zhang wrote:
> > > Mark,
> > >
> > > Thank you for your reply. EM works fine before position-restrained MD.
> > > Do you have any other suggestion besides to reduce the number of water
> > > inside the nanotube? Thanks!
> >
> > You could edit vdwradii.dat in the gromacs/share/top directory to give
> > either the water atoms or nanotube atoms more bulk for genbox - see man
> > genbox for a few details.
> >
> > Mark
> > _______________________________________________
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