hello sir,<br><br> initially i did dynamics for my protein with 30000water molecules.. it went correctly..<br><br>when i thought of reducing water i decreased my box size so that my sol number is around 70000.<br><br>when i go for energy minimisation i got its output.. but when i analysed its potential energy its coming as positive..<br>
<br>even i tried many times but i am getting positive energy ..<br><br>to have a stable system i need to have negative PE.. <br><br>this is my analysis outut<br><br><br>Opened surf_em.edr as single precision energy file<br>
<br>Select the terms you want from the following list by<br>selecting either (part of) the name or the number or a combination.<br>End your selection with an empty line or a zero.<br>-------------------------------------------------------------------<br>
1 G96Bond 2 G96Angle 3 Proper-Dih. 4 Improper-Dih. <br> 5 LJ-14 6 Coulomb-14 7 LJ-(SR) 8 Coulomb-(SR) <br> 9 Coul.-recip. 10 Potential 11 Pressure 12 Vir-XX <br>
13 Vir-XY 14 Vir-XZ 15 Vir-YX 16 Vir-YY <br> 17 Vir-YZ 18 Vir-ZX 19 Vir-ZY 20 Vir-ZZ <br> 21 Pres-XX 22 Pres-XY 23 Pres-XZ 24 Pres-YX <br>
25 Pres-YY 26 Pres-YZ 27 Pres-ZX 28 Pres-ZY <br> 29 Pres-ZZ 30 #Surf*SurfTen 31 Mu-X 32 Mu-Y <br> 33 Mu-Z 34 T-rest <br><br>10<br><br>
<br>Back Off! I just backed up energy.xvg to ./#energy.xvg.1#<br>Last energy frame read 276 time 347.000 <br><br>Statistics over 347 steps [ 1.0000 through 347.0000 ps ], 1 data sets<br>All statistics are over 277 points (frames)<br>
<br>Energy Average Err.Est. RMSD Tot-Drift<br>-------------------------------------------------------------------------------<br>Potential 270008 250000 1.01247e+06 -1.51432e+06 (kJ/mol)<br>
<br>You may want to use the -driftcorr flag in order to correct<br>for spurious drift in the graphs. Note that this is not<br>a substitute for proper equilibration and sampling!<br>You should select the temperature in order to obtain fluctuation properties.<br>
<br>gcq#336: "Ohne Arbeit wird das Leben Oede" (Wir Sind Helden)<br><br><br><br><br>can anyone please help me why its coming like this..<br><br>i am got negative value when i did initially with 300000 sol.. but now getting positive value for 70000sol..<br>
<br><br>please help me..<br><br>Thanking you,<br><br><br>