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Dear Vitaly<br><br><div><br></div><div><span class="Apple-style-span" style="font-size: 13.3333px; ">Your answer is equivalente to the 2a option of my firts e-mail.</span><br><br><div><br></div><div>Will you explain me the meaning of the -mv option.?, why not use -mv in my command line?</div><div><br></div><div>There are bit differences between the 2a and 2b option, whic is the correct?</div><div><br></div><div><br></div><div>Regards</div><div><br></div><div><br></div><div>Ricardo</div><div><br></div><div>..................................................................................................</div><div>> Date<div><span class="Apple-style-span" style="font-size: 13.3333px; ">: Mon, 28 Jun 2010 13:26:33 +0300</span></div><div>> Subject: Re: Diffusion constant<br>> From: vvchaban@gmail.com<br>> To: gmx-users@gromacs.org<br>> CC: rcuyag@hotmail.com<br>> <br>> Dear Teobaldo,<br>> <br>> I think your calculation should be as easy as:<br>> "<br>> g_msd -n index.ndx<br>> "<br>> where index.ndx contains the atom numbers belonging to that "one<br>> molecule in water".<br>> <br>> Good luck,<br>> Vitaly<br>> <br>> <br>> > Dear Users<br>> > I want to calculate the diffusion constant of one molecule in water.I make this calculation in the followin way:<br>> > Obtaining a continuos trajectory<br>> > 1) trjconv -f traj.trr -pbc nojump -o traj_nojump.xtc<br>> ><br>> > Obtaining the msd of the solute, removing the center of mass of the system<br>> > Firt way:<br>> > 2a) g_msd -f traj_nojump.xtc -s topol.tpr -n index.ndx -o msd_solute.xvg -rmcomm<br>> > I choose SOLUTE<br>> ><br>> > Second way<br>> ><br>> > 2b) g_msd -f traj_nojump.xtc -s topol.tpr -n index.ndx -rmcomm -o msd_solute.xvg -rmcomm -mv<br>> > I choose SOLUTE<br>> ><br>> > There are significative differences in the results?<br>> > according to the gromacs manual -mv option is used in molecules,<br>> ><br>> > What is the correct step, 2a or 2b?<br>> ><br>> ><br>> > Regards<br>> > Teobaldo<br>> ><br></div></div></div> <br /><hr />Jeux Messenger : mettez vos amis au défi! <a href='http://go.microsoft.com/?linkid=9734391' target='_new'>Jeux Messenger!</a></body>
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