<div>Dear Peter,</div> <div> </div> <div>Thank you very much for your reply. I agree that I did spelling mistake in this MD mdp file. But I tried two more MD runs with simulated annealing. One from the manual (example parameters I used) and the another one in which I gave the parameters on my own. But in both the cases there is no spelling mistake. But When I run the grompp program it shows warning for the simulated annealing parameters and runs with the reference temperature as I mentioned in my previous mail. </div> <div> </div> <div>Thanks once again,</div> <div> </div> <div>With prayers</div> <div>Poornima</div> <div> </div> <div><BR><B><I>Peter Friedel <friedel@ipfdd.de></I></B> wrote:</div> <BLOCKQUOTE class=replbq style="PADDING-LEFT: 5px; MARGIN-LEFT: 5px; BORDER-LEFT: #1010ff 2px solid">dear poornima,<BR><BR>I saw the parameterfile and could see that the word<BR><BR>"annel" (your choice) is not the
right<BR>"anneal"<BR><BR>can you see it too ...?<BR>sincerely, peter<BR><BR>Dr. Peter Friedel<BR>Hohe Str. 6, 01069 Dresden<BR>Institut für Polymerforschung Dresden e.V.<BR>Tel.: 0351-4658289<BR>Fax: 0351-4658565<BR>email: friedel@ipfdd.de<BR>>>> poornings@yahoo.co.in 29.03.06 13.02 >>><BR>Dear GMX users,<BR><BR>We are using GROMACS version 3.2.1. I am trying to do<BR>simulated annealing. But when I use the following <BR>parameters and do the MD, it is working with the<BR>reference temperature and not with which is given in<BR>the parameter file.. <BR><BR>And I tried with the example parameters which is given<BR>in the manual(version 3.2). For that MD also the job<BR>running with the reference temperature and not with<BR>the parameters from the *.mdp file. In both MD runs<BR>the temperature starts with 0K and drastically<BR>increases to 300 K and stays there as shown below.<BR><BR>this is my md.mdp file <BR><BR><BR>; Input file<BR>;<BR>title = Simulated annealing
<BR>cpp = /lib/cpp<BR>constraints = all-bonds<BR>integrator = md<BR>dt = 0.002 ; ps !<BR>nsteps = 5000 ; total 10 ps.<BR>nstcomm = 1<BR>nstxout = 50<BR>nstvout = 10<BR>nstfout = 0<BR>nstlog = 10<BR>nstenergy = 10<BR>nstlist = 10<BR>ns_type = grid<BR>rlist = 1.0<BR>rcoulomb = 1.0<BR>rvdw = 1.0<BR>; Berendsen temperature coupling is on in two groups<BR>Tcoupl = berendsen<BR>tc-grps = Protein SOL<BR>tau_t = 0.1 0.1<BR>ref_t = 300 300<BR>; Energy monitoring<BR>energygrps = Protein SOL<BR>; Isotropic pressure coupling is now on<BR>Pcoupl = berendsen<BR>Pcoupltype = isotropic<BR>tau_p = 0.5<BR>compressibility = 4.5e-5<BR>ref_p = 1.0<BR>;simulated annealing<BR>anneling = single<BR>anneling_npoints = 5 <BR>anneling_time = 2 4 6 8 10<BR>anneling_temp = 320 338 350 360 370<BR>; Generate velocites is off at 300 K.<BR>gen_vel = no<BR>gen_temp = 300.0<BR>gen_seed = 173529<BR><BR><BR>Temperature file:<BR><BR><BR>@ s0 legend "Temperature"<BR>0.000000 0.086951<BR>0.200000 220.175079<BR>0.400000
262.944397<BR>0.600000 282.395752<BR>0.800000 293.998444<BR>1.000000 298.549774<BR>1.200000 300.120056<BR>1.400000 299.403503<BR>1.600000 303.405151<BR>1.800000 301.161957<BR>2.000000 304.617310<BR>2.200000 303.537720<BR>2.400000 302.279572<BR>2.600000 303.867737<BR>2.800000 302.275452<BR>3.000000 301.493378<BR>3.200000 301.526245<BR>3.400000 303.736694<BR>3.600000 301.757965<BR>3.800000 303.026459<BR>4.000000 303.397949<BR>4.200000 302.376648<BR>4.400000 303.217651<BR>4.600000 302.399109<BR>4.800000 300.652893<BR>5.000000 303.834076<BR>5.200000 301.243988<BR>5.400000 301.688507<BR>5.600000 302.610657<BR>5.800000 301.640869<BR>6.000000 304.499786<BR>6.200000 300.827179<BR>6.400000 301.871277<BR>6.600000 303.083862<BR>6.800000 301.232208<BR>7.000000 302.402039<BR>7.200000 301.419037<BR>7.400001 302.663788<BR>7.600000 302.595581<BR>7.800000 302.314087<BR>8.000000 302.684509<BR>8.200001 301.203461<BR>8.400001 302.746521<BR>8.600000 303.401215<BR>8.800000 300.715942<BR>9.000000
303.033508<BR>9.200001 303.863403<BR>9.400001 302.107880<BR>9.600000 301.958099<BR>9.800000 301.676819<BR>10.000000 300.723846<BR><BR><BR>can anybody help me to soft out this problem!!<BR><BR>Thanks in advance. <BR><BR>With prayers<BR>Poornima<BR><BR><BR><BR>__________________________________________________________ <BR>Yahoo! India Matrimony: Find your partner now. Go to http://yahoo.shaadi.com<BR>_______________________________________________<BR>gmx-users mailing list gmx-users@gromacs.org<BR>http://www.gromacs.org/mailman/listinfo/gmx-users<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 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></BLOCKQUOTE><BR><p>
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