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Hi,<br><br>So the system seems to be stable now?<br><br>The water molecules might get a very small velocity, because constraints are always applied.<br>If your starting coordinates do not have full precision (e.g. gro or pdb), a minor correction<br>and thus velocity will occur at step 0 only. This should not be an issue.<br><br>Berk<br><br><hr id="stopSpelling">Date: Sun, 25 Apr 2010 11:59:36 -0400<br>Subject: Re: [gmx-users] RE: [Bug 404] energy increase in nvt and nve simiulations<br>From: jampanis@gmail.com<br>To: gmx-users@gromacs.org<br><br>Dear Berk, <br><br>First of all thanks very much for your kind patience and help. As a new user i am facing some problems and not clear about many options and how to use them. I was reading several messages of yours from mailing list which are very close to my problem. <br>
After reading several of them from mailing list i have carefully tuned my md.mdp file and the energy out put from g_energy is here.<br><br>+++++++++++++++++++++++++++++++++++++++++++++++++++<br><br>Last energy frame read 1000 time 2000.000<br>
<br>Statistics over 1000001 steps [ 0.0000 thru 2000.0001 ps ], 1 data sets<br>All averages are exact over 1000001 steps<br><br>Energy Average RMSD Fluct. Drift Tot-Drift<br>-------------------------------------------------------------------------------<br>
Total Energy -55074.6 348.391 347.979 -0.0293271 -58.6543<br>+++++++++++++++++++++++++++++++++++++++++++++++++++++++<br><br>Energy looks pretty stable compare to the one i have reported in Bugzilla, in which i always use to get the drift from 200 to 600, and finally it ends up with positive energy.<br>
<br>Here is the md.mdp file i have used for my current simulation.<br><br>++++++++++++++++++++++++++++++++++++++++++++<br>title = AB2130<br>cpp = /usr/bin/cpp<br>constraints = all-bonds<br>integrator = md<br>
dt = 0.002 ; ps !<br>nsteps = 1000000 ; total 100.0 ns.<br>nstxout = 1000 ; collect data every 2.0 ps<br>nstvout = 1000 ; collect velocity every 2.0 ps<br>nstfout = 0<br>nstlog = 0<br>
comm_mode = none<br>nstenergy = 1000 ; collect energy every 2.0 ps<br>nstlist = 10<br>ns_type = grid<br>pbc = xyz<br>rlist = 1.0<br>coulombtype = cut-off<br>rcoulomb = 1.0<br>
rvdw = 1.0<br>rvdw_switch = 0.9<br>fourierspacing = 0.12<br>fourier_nx = 0<br>fourier_ny = 0<br>fourier_nz = 0<br>optimize_fft = yes<br>; Berendsen temperature coupling is on in two groups<br>
Tcoupl = V-rescale<br>tau_t = 0.1 0.1<br>tc-grps = Tmp1 Tmp2<br>ref_t = 283.0 0.0<br>;Generate velocites is on at 300 K.<br>gen_vel = yes<br>gen_temp = 283.0<br>
energygrps = Tmp1 Tmp2<br>energygrp_excl = Tmp2 Tmp2 Tmp2 Tmp1<br>gen_seed = 181726<br>freezegrps = Tmp2<br>freezedim = Y Y Y<br>+++++++++++++++++++++++++++++++++++++++++++++++<br><br>I still have small question here, when i try to print the velocities from trajectory i found that some of the frozen water too get the velocities (i have complied my gromcas with md.c Fixed velocity output at first step on nodes>1 with PD and frozen groups). <br>
<br>Here is the example for few frozen water.<br><br>++++++++++++++++++++++++++++++++++++++++++++++<br> 48SOL OW 149 1.630 1.491 6.061 -0.0001 -0.0000 -0.0000<br> 48SOL HW1 150 1.555 1.541 6.027 -0.0001 0.0001 -0.0000<br>
.<br>.<br>.<br> 9503SOL OW31669 6.075 6.430 0.097 0.0001 0.0000 -0.0000<br> 9503SOL HW131670 5.984 6.437 0.126 0.0000 0.0001 -0.0000<br> 9503SOL HW231671 6.089 6.508 0.044 -0.0001 0.0001 -0.0000<br>
++++++++++++++++++++++++++++++++++++++++++++++++++<br><br>I am not very clear why i am still getting this velocity, and how would these velocities to frozen atoms effect the simulation?<br><br>Can you please give me your suggestions.<br>
<br>Thanks in advance<br>Srinivas.<br><br clear="all"><br>-- <br>*********************************************<br>J. Srinivasa Rao <br>Post-doctoral Research Associate<br>C/o Prof. Luis R Cruz Cruz<br>Computational Biophysics Group<br>
Department of Physics<br>Drexel University<br>3141 Chestnut St<br>Philadelphia, PA 19104, USA.<br>Ph: Off: 215-895-1989<br> Mob: 704-706-4191<br>**********************************************<br><br><br> <br /><hr />New Windows 7: Find the right PC for you. <a href='http://windows.microsoft.com/shop' target='_new'>Learn more.</a></body>
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