<HTML><HEAD><META content="text/html; charset=x-user-defined" http-equiv="Content-Type"><style type="text/css"><!--.MailHeader { font-family: "Arial"; font-size: 8pt; color: #000000; font-style: normal; font-weight: normal; text-decoration: none; }//--></style></HEAD><BODY><p><br ><strong>Thankyou for the reply Mark. In fact I started another simulated annealing job for my peptide with Tcoupl = Berendsen using the same annealing protocol. I didnot get any warnings. However the temperature increases from 0 to 53K and fluctuates around that through out till the end of the simulation. I am attaching the Averages and RMS values for the various components that its calculating. As you can see the average Temp is around 56 -58. Why is this not increasing beyound that? I would also like to know if the RMS fluctuations are in the required range , further if the system is behaving as an NVE ensemble which I don't intend to do right now what parameters I should correct in order to achieve an NPT ensemble. Density of methanol is maintained, however the box sizes are reduced slightly from (editconf -f 2MLT_pdb2gmx.gro -o 2MLT_box.gro -bt octahedron -box 6.9 6.9 6.9) to the ones as shown below. Kindly guide me through.<br ><br >Regards<br >sharada<br ><br ></strong><br >############# ==><br > <==== A V E R A G E S ====><br > <== ############### ======></p><p>Current ref_t for group Protein: 300.0<br >Current ref_t for group Other: 300.0<br > Energies (kJ/mol)<br > Angle G96Angle Proper Dih. Improper Dih. LJ-14<br > 1.25569e+02 1.45264e+02 8.14163e+01 3.35938e+01 -4.14588e+00<br > Coulomb-14 LJ (SR) LJ (LR) Coulomb (SR) Coul. recip.<br > 1.11566e+02 -6.13052e+04 -9.02963e+02 -4.90858e+02 -2.29446e+02<br > Potential Kinetic En. Total Energy Temperature Pressure (bar)<br > -6.24352e+04 6.55473e+03 -5.58804e+04 5.61922e+01 -6.44581e-01</p><p> Box-X Box-Y Box-Z Volume Density (SI)<br > 6.59352e+00 6.21552e+00 5.38142e+00 2.20549e+02 9.71762e+02<br > pV<br > -1.00030e+01</p><p> Total Virial (kJ/mol)<br > 2.20235e+03 1.73889e+01 3.30993e+01<br > 1.73889e+01 2.19217e+03 3.10533e+01<br > 3.30993e+01 3.10533e+01 2.17521e+03</p><p> Pressure (bar)<br > -3.38055e+00 -2.23803e+00 -5.33957e+00<br > -2.23802e+00 -6.64252e-01 -4.91175e+00<br > -5.33957e+00 -4.91175e+00 2.11106e+00</p><p> Total Dipole (Debye)<br > 1.27755e+02 3.52104e+02 3.75237e+02</p><p> Epot (kJ/mol) Coul-SR LJ-SR LJ-LR Coul-14 LJ-14 <br >Protein-Protein -3.40720e+01 -6.16549e+02 -2.13677e+00 1.11566e+02 -4.14588e+00<br > Protein-Other -1.39464e+01 -1.18676e+03 -3.93175e+01 0.00000e+00 0.00000e+00<br > Other-Other -4.42840e+02 -5.95019e+04 -8.61509e+02 0.00000e+00 0.00000e+00</p><p> T-Protein T-Other<br > 5.81959e+01 5.61543e+01</p><p> <====== ############################### ==><br > <==== R M S - F L U C T U A T I O N S ====><br > <== ############################### ======></p><p>Current ref_t for group Protein: 300.0<br >Current ref_t for group Other: 300.0<br > Energies (kJ/mol)<br > Angle G96Angle Proper Dih. Improper Dih. LJ-14<br > 3.63607e+00 8.07621e+00 5.91745e+00 3.68058e+00 6.03747e+00<br > Coulomb-14 LJ (SR) LJ (LR) Coulomb (SR) Coul. recip.<br > 3.94884e-01 5.68584e+02 7.51264e+00 2.60823e+01 5.45860e+00<br > Potential Kinetic En. Total Energy Temperature Pressure (bar)<br > 6.06744e+02 3.31755e+02 9.21157e+02 2.84406e+00 2.89776e+01</p><p> Box-X Box-Y Box-Z Volume Density (SI)<br > 2.05639e-02 1.97767e-02 1.78224e-02 2.14976e+00 9.09307e+00<br > pV<br > 4.03650e+02</p><p> Total Virial (kJ/mol)<br > 3.48732e+02 2.38190e+02 2.34143e+02<br > 2.38190e+02 3.58063e+02 2.29927e+02<br > 2.34143e+02 2.29927e+02 3.69445e+02</p><p> Pressure (bar)<br > 4.96979e+01 3.61135e+01 3.53962e+01<br > 3.61135e+01 5.04350e+01 3.47331e+01<br > 3.53962e+01 3.47331e+01 5.09166e+01</p><p> Total Dipole (Debye)<br > 8.26716e+01 8.83756e+01 9.41694e+01</p><p> Epot (kJ/mol) Coul-SR LJ-SR LJ-LR Coul-14 LJ-14 <br >Protein-Protein 8.03847e-01 5.52640e+00 5.38082e-02 3.94884e-01 6.03747e+00<br > Protein-Other 2.33155e+00 1.42410e+01 4.03903e-01 0.00000e+00 0.00000e+00<br > Other-Other 2.54858e+01 5.55314e+02 7.27596e+00 0.00000e+00 0.00000e+00</p><p> T-Protein T-Other<br > 4.00791e+00 2.87110e+00</p><p><br ></p><font face="Arial" size="2"><TABLE STYLE="PADDING-LEFT: 5px; BORDER-BOTTOM-COLOR: blue; BORDER-LEFT: blue 1px solid; BORDER-TOP-COLOR: blue; BORDER-RIGHT-COLOR: blue"><tbody><TR><TD><br ><strong><em>-- Original Message --</em></strong><br >From: Mark Abraham <Mark.Abraham@anu.edu.au><br >To: Discussion list for GROMACS users <gmx-users@gromacs.org><br >Date: Fri, 13 Feb 2009 00:13:23 +1100<br >Subject: Re: [gmx-users] SIMULATED ANNEALING<br ><br >sharada wrote:<br >> Dear Nuno Azoia,<br >> <br >> I followed one of the replies given at gmx-users list which I quote <br >> here...I donot know whether this is right ? In that case the temperature <br >> has truly changed from 0 to 60 how is it possible if Tcoupl = no...?I <br >> am in doubt.<br ><br >You're actually running in an NVE ensemble, which hasn't yet reached its <br >natural equilibrium temperature.<br ><br >Perhaps there should be a grompp warning for when simulated annealing is <br >attempted without temperature coupling...<br ><br >Mark<br >_______________________________________________<br >gmx-users mailing list gmx-users@gromacs.org<br >http://www.gromacs.org/mailman/listinfo/gmx-users<br >Please search the archive at http://www.gromacs.org/search before posting!<br >Please don't post (un)subscribe requests to the list. Use the <br >www interface or send it to gmx-users-request@gromacs.org.<br >Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br ></TD></TR></tbody></TABLE></font></BODY></HTML>