Gaurav Chopra wrote:
/ Hi
/>/
/>/ I get the following error when using mdrun for a protein in
solution. />/ I have checked the structure and everything looks fine
to me. Could />/ you suggested anything else I could do. /
How did you energy minimze your structure? What was the output of
mdrun during energy minization, especially the last line with Fmax,
Epot etc.?
I should look like this:
Step= 48, Dmax= 1.1e-02 nm, Epot= -1.45545e+06 Fmax= 5.58480e+05,
atom= 78754
Step= 49, Dmax= 1.4e-02 nm, Epot= -1.45551e+06 Fmax= 8.80803e+03,
atom= 13032
Step= 50, Dmax= 1.7e-02 nm, Epot= -1.45574e+06 Fmax= 1.60758e+04,
atom= 13032
Jochen
Hi Gaurav,
what is your stepsize during the simulation? what is constrained? And
have you run a minimization before starting the simulation?
hear from you soon
Steffen
Hi
For the initial mdrun, (i.e. energy min before the actual md) the log
file output (last part is). After this em step I use grompp with my
final mdp file and then mdrun where I get the LINCS error.
Thanks
gaurav
Energies (kJ/mol)
Bond Angle Proper Dih. Ryckaert-Bell. LJ-14
3.35740e+03 1.35497e+03 4.60212e+01 8.38627e+02 1.33998e+03
Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. Potential
4.11813e+03 5.16092e+04 -3.42126e+05 -3.63260e+04 -3.15787e+05
Kinetic En. Total Energy Temperature Pressure (bar)
0.00000e+00 0.00000e+00 0.00000e+00 0.00000e+00
Step Time Lambda
165 165.00000 0.00000
Step Time Lambda
166 166.00000 0.00000
Step Time Lambda
167 167.00000 0.00000
Energies (kJ/mol)
Bond Angle Proper Dih. Ryckaert-Bell. LJ-14
3.35747e+03 1.35504e+03 4.60229e+01 8.38637e+02 1.33998e+03
Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. Potential
4.11748e+03 5.16092e+04 -3.42126e+05 -3.63260e+04 -3.15788e+05
Kinetic En. Total Energy Temperature Pressure (bar)
0.00000e+00 0.00000e+00 0.00000e+00 0.00000e+00
Step Time Lambda
168 168.00000 0.00000
Step Time Lambda
169 169.00000 0.00000
Step Time Lambda
170 170.00000 0.00000
Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax < 10
Double precision normally gives you higher accuracy.
You might need to increase your constraint accuracy, or turn
off constraints alltogether (set constraints = none in mdp file)
Steepest Descents converged to machine precision in 171 steps,
but did not reach the requested Fmax < 10.
Potential Energy = -3.1578772e+05
Maximum force = 5.0164816e+04 on atom 897
Norm of force = 1.1000233e+05
M E G A - F L O P S A C C O U N T I N G
RF=Reaction-Field FE=Free Energy SCFE=Soft-Core/Free Energy
T=Tabulated W3=SPC/TIP3p W4=TIP4p (single or pairs)
NF=No Forces
Computing: M-Number M-Flops % of Flops
-----------------------------------------------------------------------
Coul(T) 20.674176 868.315392 1.8
Coul(T) [W3] 0.311534 38.941750 0.1
Coul(T) + LJ 19.239903 1058.194665 2.2
Coul(T) + LJ [W3] 3.200326 441.644988 0.9
Coul(T) + LJ [W3-W3] 78.699237 30063.108534 62.8
Outer nonbonded loop 8.258931 82.589310 0.2
1,4 nonbonded interactions 0.413991 37.259190 0.1
Spread Q Bspline 234.956736 469.913472 1.0
Gather F Bspline 234.956736 2819.480832 5.9
3D-FFT 723.824532 5790.596256 12.1
Solve PME 10.687500 684.000000 1.4
NS-Pairs 214.955143 4514.058003 9.4
Reset In Box 3.671199 33.040791 0.1
Shift-X 3.670515 22.023090 0.0
CG-CoM 1.225386 35.536194 0.1
Bonds 0.159714 6.867702 0.0
Angles 0.287622 46.882386 0.1
Propers 0.030780 7.048620 0.0
RB-Dihedrals 0.320625 79.194375 0.2
Settle 2.340990 756.139770 1.6
-----------------------------------------------------------------------
Total 47854.835320 100.0
-----------------------------------------------------------------------
NODE (s) Real (s) (%)
Time: 50.000 50.000 100.0
Finished mdrun on node 0 Wed Mar 8 06:13:35 2006
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