<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>Dear Nuno Azoia,</p><p>I followed one of the replies given at gmx-users list which I quote here...I donot know whether this is right ? In that case the temperature has truly changed from 0 to 60 how is it possible if Tcoupl = no...?I am in doubt.</p><p>Kindly comment. <br >sharada</p><p><br ><em><strong>Re: [gmx-users] how to write a annealing .mdp<br >Qiao Baofu<br >Wed, 13 Sep 2006 05:04:30 -0700</strong></em></p><p><em><strong>Hi,<br > set T_couple=no and refer to the following script</strong></em></p><p><em><strong>; SIMULATED ANNEALING <br >; Type of annealing for each temperature group (no/single/periodic)<br >annealing = single<br >; Number of time points to use for specifying annealing in each group <br >annealing_npoints = 6<br >; List of times at the annealing points for each group<br >annealing_time = 0 10 20 30 40 50<br >; Temp. at each annealing point, for each group.<br >annealing_temp = 425 375 325 275 245 203 </strong></em></p><p><br ><em><strong>06-9-13zzhwise1 <[EMAIL PROTECTED]> <br >hello everyone<br > i want to anneal my system,but i don't konw how to wrote a right annealing-mdp!<br >could anyone give me a moldel?<br > tanks in advaced!<br ></strong></em></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: Nuno Azoia <nazoia@det.uminho.pt><br >To: Discussion list for GROMACS users <gmx-users@gromacs.org><br >Date: Thu, 12 Feb 2009 12:22:43 +0000<br >Subject: Re: [gmx-users] (no subject)<br ><br >I don't have so much experience, but I found something strange in our<br >mdp file.<br ><br >>; Berendsen temperature coupling is on in two groups<br >> Tcoupl = no<br >> tau_t = 0 0<br ><br >In my opinion, I think that if you have Tcoupl = no you can't expect the<br >temperature of your system to chage.<br ><br >Nuno Azoia<br ><br >On Thu, 2009-02-12 at 17:32 +0530, sharada wrote:<br >> Dear gromacs-users,<br >> <br >> I am heating a peptidein methanol from 0K - 300K. The simulated<br >> annealing protocol is given in the md.mdp file shown below:<br >> <br >> ------------------------------------------------<br >> title = cpeptide MD<br >> cpp = /lib/cpp<br >> constraints = all-bonds<br >> integrator = md<br >> tinit = 0.0<br >> dt = 0.002 ; ps !leapfrog algorithm 2fs timestep<br >> nsteps = 500000 ; total 2 ns.<br >> nstcomm = 1<br >> nstxout = 10000<br >> nstvout = 5000<br >> nstfout = 0<br >> nstlist = 5<br >> ns_type = grid<br >> pbc = xyz<br >> coulombtype = PME<br >> rlist = 1.2<br >> rcoulomb = 1.2<br >> rvdw = 1.5<br >> epsilon_r = 32.0<br >> ; Berendsen temperature coupling is on in two groups<br >> Tcoupl = no<br >> tau_t = 0 0<br >> tc-grps = protein other<br >> ref_t = 50 50<br >> solvent_optimization = sol<br >> ; Energy monitoring<br >> energygrps = Protein other<br >> ; Pressure coupling is on<br >> Pcoupl = Berendsen<br >> tau_p = 0.5<br >> compressibility = 4.5e-5<br >> ref_p = 1.0<br >> <br >> ; SIMULATED ANNEALING <br >> ; Type of annealing for each temperature group (no/single/periodic)<br >> annealing = single single<br >> ; Number of time points to use for specifying annealing in each group<br >> annealing_npoints = 9 9<br >> ; List of times at the annealing points for each group<br >> annealing_time = 0 10 20 30 40 50 60 70 80 0 10 20 30 40 50<br >> 60 70 80<br >> ; Temp. at each annealing point, for each group.<br >> annealing_temp = 50 80 110 140 170 200 230 260 300 50 80 110<br >> 140 170 200 230 260 300 <br >> <br >> <br >> ; Generate velocites is on at 50 K.<br >> gen_vel = no<br >> gen_temp = 50.0<br >> gen_seed = 173529<br >> <br >> ----------------------------------------------<br >> <br >> This is the output of the run ...<br >> <br >> Current ref_t for group Protein: 50.0<br >> Current ref_t for group Other: 50.0<br >> Energies (kJ/mol)<br >> Angle G96Angle Proper Dih. Improper Dih.<br >> LJ-14<br >> 1.51438e+02 1.57246e+02 9.67560e+01 3.39340e+01<br >> -1.86728e+00<br >> Coulomb-14 LJ (SR) LJ (LR) Coulomb (SR) Coul.<br >> recip.<br >> 1.11363e+02 -5.80246e+04 -8.11824e+02 -4.91976e+02<br >> -2.26900e+02<br >> Potential Kinetic En. Total Energy Temperature Pressure<br >> (bar)<br >> -5.90065e+04 5.82281e+03 -5.31836e+04 4.99176e+01<br >> -1.00344e+03<br >> <br >> Step Time Lambda<br >> 100 0.20000 0.00000<br >> <br >> Rel. Constraint Deviation: Max between atoms RMS<br >> Before LINCS 0.002846 58 59 0.000439<br >> After LINCS 0.000010 105 107 0.000001<br >> <br >> Current ref_t for group Protein: 50.6<br >> Current ref_t for group Other: 50.6<br >> Energies (kJ/mol)<br >> Angle G96Angle Proper Dih. Improper Dih.<br >> LJ-14<br >> 1.38141e+02 1.48331e+02 1.05076e+02 3.22396e+01<br >> -3.30152e+00<br >> Coulomb-14 LJ (SR) LJ (LR) Coulomb (SR) Coul.<br >> recip.<br >> 1.10745e+02 -5.83654e+04 -8.23368e+02 -4.82819e+02<br >> -2.28454e+02<br >> Potential Kinetic En. Total Energy Temperature Pressure<br >> (bar)<br >> -5.93689e+04 5.94610e+03 -5.34228e+04 5.09746e+01<br >> -7.78032e+02<br >> <br >> Step Time Lambda<br >> 200 0.40000 0.00000<br >> <br >> Rel. Constraint Deviation: Max between atoms RMS<br >> Before LINCS 0.003484 5534 5535 0.000426<br >> After LINCS 0.000007 66 67 0.000001<br >> <br >> Current ref_t for group Protein: 51.2<br >> Current ref_t for group Other: 51.2<br >> Energies (kJ/mol)<br >> Angle G96Angle Proper Dih. Improper Dih.<br >> LJ-14<br >> 1.43780e+02 1.37908e+02 1.03575e+02 3.10259e+01<br >> 2.92268e+00<br >> Coulomb-14 LJ (SR) LJ (LR) Coulomb (SR) Coul.<br >> recip.<br >> 1.11216e+02 -5.86508e+04 -8.31542e+02 -4.89405e+02<br >> -2.23838e+02<br >> Potential Kinetic En. Total Energy Temperature Pressure<br >> (bar)<br >> -5.96652e+04 6.12069e+03 -5.35445e+04 5.24713e+01<br >> -4.88928e+02<br >> <br >> Step Time Lambda<br >> 300 0.60000 0.00000<br >> <br >> Rel. Constraint Deviation: Max between atoms RMS<br >> Before LINCS 0.002752 5792 5793 0.000424<br >> After LINCS 0.000008 105 107 0.000001<br >> <br >> Current ref_t for group Protein: 51.8<br >> Current ref_t for group Other: 51.8<br >> Energies (kJ/mol)<br >> Angle G96Angle Proper Dih. Improper Dih.<br >> LJ-14<br >> 1.48813e+02 1.42970e+02 1.03284e+02 3.23617e+01<br >> -4.37215e+00<br >> Coulomb-14 LJ (SR) LJ (LR) Coulomb (SR) Coul.<br >> recip.<br >> 1.11596e+02 -5.88305e+04 -8.37264e+02 -4.92025e+02<br >> -2.29802e+02<br >> Potential Kinetic En. Total Energy Temperature Pressure<br >> (bar)<br >> -5.98550e+04 6.24111e+03 -5.36139e+04 5.35036e+01<br >> -2.18755e+02<br >> <br >> Step Time Lambda<br >> 400 0.80000 0.00000<br >> <br >> Rel. Constraint Deviation: Max between atoms RMS<br >> Before LINCS 0.003186 5135 5136 0.000428<br >> After LINCS 0.000007 45 46 0.000001<br >> <br >> Current ref_t for group Protein: 52.4<br >> Current ref_t for group Other: 52.4<br >> Energies (kJ/mol)<br >> Angle G96Angle Proper Dih. Improper Dih.<br >> LJ-14<br >> 1.48258e+02 1.34671e+02 9.78242e+01 3.23113e+01<br >> 2.68271e+00<br >> Coulomb-14 LJ (SR) LJ (LR) Coulomb (SR) Coul.<br >> recip.<br >> 1.11526e+02 -5.88899e+04 -8.39509e+02 -5.12034e+02<br >> -2.29234e+02<br >> Potential Kinetic En. Total Energy Temperature Pressure<br >> (bar)<br >> -5.99434e+04 6.28344e+03 -5.36599e+04 5.38665e+01<br >> -8.48820e+01<br >> <br >> Step Time Lambda<br >> 500 1.00000 0.00000<br >> <br >> Rel. Constraint Deviation: Max between atoms RMS<br >> Before LINCS 0.003304 7457 7458 0.000434<br >> After LINCS 0.000007 189 190 0.000001<br >> <br >> ---<br >> ---<br >> ---<br >> ---<br >> 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.<br >> LJ-14<br >> 1.32540e+02 1.42359e+02 8.84796e+01 3.64486e+01<br >> 2.81073e+00<br >> Coulomb-14 LJ (SR) LJ (LR) Coulomb (SR) Coul.<br >> recip.<br >> 1.11433e+02 -6.05890e+04 -8.96227e+02 -4.56756e+02<br >> -2.26580e+02<br >> Potential Kinetic En. Total Energy Temperature Pressure<br >> (bar)<br >> -6.16545e+04 7.10020e+03 -5.45543e+04 6.08684e+01<br >> -2.20348e+01<br >> <br >> ---------------------------------------------------------------------------<br >> <br >> The problem is the temperature of the system is remaining at 60K even<br >> when ref_t goes to 300K. I have shown some portion of the output for<br >> your information. Why is this happening ? Kindly help.<br >> <br >> thankyou <br >> <br >> sharada<br >> <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 ><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>