Dear Carlos,
The RMSD between the initial and final structure was15.374. The protein was
moving towards the final pose.
At the end step of the simulation result is
NSTEP = 25000 TIME(PS) = 125.000 TEMP(K) = 300.07 PRESS =
18.6
Etot = -1010255.9572 EKtot = 289179.9513 EPtot =
-1299435.9085
BOND = 14201.0200 ANGLE = 52898.5640 DIHED =
31543.0883
1-4 NB = 13358.7775 1-4 EEL = -143960.7010 VDWAALS =
136790.5034
EELEC = -1407440.5066 EHBOND = 0.0000 RESTRAINT =
1864.7033
EAMBER (non-restraint) = -1301300.6117
EKCMT = 109285.4199 VIRIAL = 107397.5072 VOLUME =
4692401.4722
SURFTEN =
-50.4288
CMAP = 1308.6427
Density =
0.9845
Ewald error estimate: 0.5038E-04
Current RMSD from reference: 6.085
Current target RMSD: 0.000
------------------------------------------------------------------------------
A V E R A G E S O V E R 25000 S T E P S
NSTEP = 25000 TIME(PS) = 125.000 TEMP(K) = 300.21 PRESS =
1.7
Etot = -1008742.2826 EKtot = 289309.2538 EPtot =
-1298051.5363
BOND = 14165.1395 ANGLE = 52797.6975 DIHED =
31725.2004
1-4 NB = 13372.2128 1-4 EEL = -143935.4507 VDWAALS =
137548.7028
EELEC = -1408624.2793 EHBOND = 0.0000 RESTRAINT =
3589.6065
EAMBER (non-restraint) = -1301641.1428
EKCMT = 109251.6375 VIRIAL = 109078.8946 VOLUME =
4695220.8457
SURFTEN =
22.5679
CMAP = 1309.6342
Density =
0.9839
Ewald error estimate: 0.2472E-04
Current RMSD from reference: 6.085
Current target RMSD: 0.000
------------------------------------------------------------------------------
R M S F L U C T U A T I O N S
NSTEP = 25000 TIME(PS) = 125.000 TEMP(K) = 0.57 PRESS =
36.7
Etot = 3461.7944 EKtot = 548.2237 EPtot =
3112.5298
BOND = 97.4918 ANGLE = 194.0957 DIHED =
162.4124
1-4 NB = 49.5120 1-4 EEL = 114.6908 VDWAALS =
527.6060
EELEC = 1076.8994 EHBOND = 0.0000 RESTRAINT =
2154.4398
EAMBER (non-restraint) = 958.0900
EKCMT = 290.1392 VIRIAL = 3723.4229 VOLUME =
3241.7672
SURFTEN =
105.5822
CMAP = 24.9993
Density =
0.0007
Ewald error estimate: 0.1559E-04
Current RMSD from reference: 6.085
Current target RMSD: 0.000
The force constant is small because of bad energy error with higher
tgtmdfrc value(tgtmdfrc>2).
I also tried with different tgtmdfrc between 1 to 0.005 and the lowest rmsd
I ever observed is around 2. I also increased the nstlim but the initial
confirmation never reached the final conformational state.
Another reason for assigning a small tgtmdfrc was to minutely observe the
conformational changes occuring in the structure.
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Received on Wed Jan 26 2022 - 23:30:02 PST
