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<DIV><FONT size=2 face=Arial><SPAN class=093293414-27042011>Dear
gmx-users,</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN class=093293414-27042011>since I'm sending my
simulations to a system with a queue with a wallclock time of 24 h, I
necessarily have to simulate small parts of my simulation, that I "stick"
together at the end with trjconv. To continue my simulations, I'm using the .cpt
file. Here my settings concerning the number of steps, dt etc. Since I started
the full MD after 20 ps NVT and 100 ps NPT I set the </SPAN></FONT><FONT size=2
face=Arial><SPAN class=093293414-27042011>mdp file as:</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN
class=093293414-27042011></SPAN></FONT> </DIV>
<DIV><FONT size=2 face=Arial><SPAN class=093293414-27042011>integrator =
md</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN class=093293414-27042011>dt =
0.002</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN class=093293414-27042011>nsteps = 2500000
(total 5 ns - the max time compatible with the wallclock
time)</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN class=093293414-27042011>init_step = 70000
(the last step after NVT+NPT)</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN class=093293414-27042011>tinit =
0</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN
class=093293414-27042011>nstxout,vout,fout,log,energy: 50000</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN
class=093293414-27042011></SPAN></FONT> </DIV>
<DIV><FONT size=2 face=Arial><SPAN class=093293414-27042011>In the command to
launch the MD simulation I set:</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN class=093293414-27042011>mpirun -np 32 -s
1R3Afull.tpr -deffnm 1R3Afull -cpt 60</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN
class=093293414-27042011></SPAN></FONT> </DIV>
<DIV><FONT size=2 face=Arial><SPAN class=093293414-27042011>After the first 5 ns
of simulation, I obtained all the files expected, and I extended the trajectory
of further 5 ns using the command:</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN class=093293414-27042011>tpbconv -s
1R3Afull.tpr -extend 5000 -o 1R3Afull2.tpr</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN
class=093293414-27042011></SPAN></FONT> </DIV>
<DIV><FONT size=2 face=Arial><SPAN
class=093293414-27042011>and</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN
class=093293414-27042011></SPAN></FONT> </DIV>
<DIV><FONT size=2 face=Arial><SPAN class=093293414-27042011>mpirun -np 32 -s
1R3Afull2.tpr -cpi 1R3Afull.cpt -deffnm 1R3Afull2 -cpt 60</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN
class=093293414-27042011></SPAN></FONT> </DIV>
<DIV><FONT size=2 face=Arial><SPAN class=093293414-27042011>I repeated the
procedure until I obtained 20 ns trajectory.</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN
class=093293414-27042011></SPAN></FONT> </DIV>
<DIV><FONT size=2 face=Arial><SPAN class=093293414-27042011>Then, I used trjcat
to concatenate 1R3Afull.xtc + 1R3Afull2.xtc + 1R3Afull3.xtc + 1R3Afull4.xtc
creating 1R3Afull20ns.xtc and eneconv to do the same with 1R3Afull.edr +
1R3Afull2.edr + 1R3Afull3.edr + 1R3Afull4.edr, creating 1R3Afull20ns.edr. Then,
I used gmxcheck -e 1R3Afull20ns.edr to check the final .edr file. I obtained an
error message:</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN
class=093293414-27042011></SPAN></FONT> </DIV>
<DIV><FONT size=2 face=Arial><SPAN class=093293414-27042011>Checking energy file
1R3Afull20ns.edr</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial></FONT> </DIV>
<DIV><FONT size=2 face=Arial><SPAN class=093293414-27042011>Opened
1R3Afull20ns.edr as double precision energy
file<BR>frame: 0
(index 0), t:
140.000 <BR>Reading energy
frame 2 time
300.000
<BR>Timesteps at t=200 don't match (60, 100)<BR>Reading energy
frame 50 time
5100.000
<BR>Timesteps at t=5100 don't match (100, 40)</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial></FONT> </DIV>
<DIV><FONT size=2 face=Arial><SPAN class=093293414-27042011>Timesteps at t=5140
don't match (40, 60)</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial></FONT> </DIV>
<DIV><FONT size=2 face=Arial><SPAN class=093293414-27042011>Timesteps at t=5200
don't match (60, 100)<BR>Reading energy frame 100 time
10000.000
<BR>Timesteps at t=10100 don't match (100, 40)</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial></FONT> </DIV>
<DIV><FONT size=2 face=Arial><SPAN class=093293414-27042011>Timesteps at t=10140
don't match (40, 60)</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial></FONT> </DIV>
<DIV><FONT size=2 face=Arial><SPAN class=093293414-27042011>Timesteps at t=10200
don't match (60, 100)<BR>Reading energy frame 150 time
14900.000
<BR>Timesteps at t=15100 don't match (100, 40)</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial></FONT> </DIV>
<DIV><FONT size=2 face=Arial><SPAN class=093293414-27042011>Timesteps at t=15140
don't match (40, 60)</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial></FONT> </DIV>
<DIV><FONT size=2 face=Arial><SPAN class=093293414-27042011>Timesteps at t=15200
don't match (60, 100)<BR>Last energy frame read 198 time
19600.000
</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial></FONT> </DIV>
<DIV><FONT size=2 face=Arial><SPAN class=093293414-27042011>Found 199
frames.</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial></FONT> </DIV>
<DIV><FONT size=2 face=Arial><SPAN class=093293414-27042011>gcq#131: "Royale
With Cheese" (Pulp Fiction)<BR></SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN class=093293414-27042011>I don't understand
why there are so many mismatches in my file. Moreover all but one are in the
correspondence of the "junctions" I made between two consecutive 5 ns runs. Does
it depend on some settings regarding init_step or dt or tinit in the .mdp file?
Did I make correctly the continuation? Could somebody help me to find the
error?</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN class=093293414-27042011>Many thanks in
advance and best regards</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN
class=093293414-27042011>Anna</DIV></SPAN></FONT>
<DIV><FONT size=2 face=Arial><SPAN
class=093293414-27042011></SPAN></FONT> </DIV>
<DIV><FONT size=2
face=Arial>__________________________________________________________________</FONT></DIV>
<DIV align=left>
<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</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>E-mail: <A
title=mailto:amarabotti@isa.cnr.it
href="mailto:amarabotti@isa.cnr.it">amarabotti@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 site: <A
title=http://bioinformatica.isa.cnr.it/anna/anna.htm
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>"When a man with a gun meets a man with
a pen, the man with the gun is a dead man"</FONT></DIV>
<DIV align=left><FONT size=2 face=Arial>(Roberto Benigni, about Roberto
Saviano)</FONT></DIV></DIV>
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