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<DIV><FONT size=2 face=Arial><SPAN class=078403613-25082010>Dear
gmx-users,</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN class=078403613-25082010>sorry for my trivial
questions, but I didn't find an answer searching in the Gromacs web site.
</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN
class=078403613-25082010></SPAN></FONT> </DIV>
<DIV><FONT size=2 face=Arial><SPAN class=078403613-25082010>I want to generate
different trajectories on my system, and I used an .mdp file in which I set
gen_seed = -1 together with gen_vel = yes and continuation = no to do this
quickly. If I understand well, every time I launch my simulation, Gromacs will
generate a different initial velocity. My questions are:</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN
class=078403613-25082010></SPAN></FONT> </DIV>
<DIV><FONT size=2 face=Arial><SPAN class=078403613-25082010>- if I want to
launch 5 different simulation, fixing gen_seed = -1 in my .mdp file I should
obtain different results without doing every time grompp+mdrun. After the first
grompp+mdrun, I have the .tpr file that includes already the information to
generate random velocities, therefore for the second, third...etc. run I simply
have to launch mdrun using the same .tpr file, right?</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN
class=078403613-25082010></SPAN></FONT> </DIV>
<DIV><FONT size=2 face=Arial><SPAN class=078403613-25082010>- is there a way to
check for the velocities or for the random seed used? I had a look at the .log
file but I didn't find the information. g_traj generated a very big file, and
presently I have some problems to analyze it. How can I see initial
velocities?</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN
class=078403613-25082010></SPAN></FONT> </DIV>
<DIV><FONT size=2 face=Arial><SPAN class=078403613-25082010>Many thanks and best
regards</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN
class=078403613-25082010>Anna</SPAN></FONT></DIV>
<DIV> </DIV>
<DIV align=left><FONT size=2
face=Arial>____________________________________________________</FONT></DIV>
<DIV align=left><FONT size=2 face=Arial>Anna Marabotti, Ph.D.</FONT></DIV>
<DIV align=left><FONT size=2 face=Arial>Laboratory of Bioinformatics and
Computational Biology</FONT></DIV>
<DIV align=left><FONT size=2 face=Arial>Institute of Food Science,
CNR</FONT></DIV>
<DIV align=left><FONT size=2 face=Arial>Via Roma, 64</FONT></DIV>
<DIV align=left><FONT size=2 face=Arial>83100 Avellino (Italy)</FONT></DIV>
<DIV align=left><FONT size=2 face=Arial>Phone: +39 0825 299651</FONT></DIV>
<DIV align=left><FONT size=2 face=Arial>Fax: +39 0825 781585</FONT></DIV>
<DIV align=left><FONT size=2 face=Arial>Email: <A
href="mailto:anna.marabotti@isa.cnr.it">anna.marabotti@isa.cnr.it</A></FONT></DIV>
<DIV align=left><FONT size=2 face=Arial>Skype account: annam1972</FONT></DIV>
<DIV align=left><FONT size=2 face=Arial>Web page: <A
href="http://bioinformatica.isa.cnr.it/anna/anna.htm">http://bioinformatica.isa.cnr.it/anna/anna.htm</A></FONT></DIV>
<DIV align=left><FONT size=2 face=Arial></FONT> </DIV>
<DIV align=left><FONT size=2 face=Arial>"If you think you are too small to make
a difference, try sleeping with a mosquito"</FONT></DIV>
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