Hi Adriana,<br><br>Did you energy minimize your system before this?<br><br>A pretty robust regime to follow is:<br><br>1. energy minimize in vacuum<br>2. energy minimize after solvation<br>3. perform position restrained MD
<br>4. run a short simulation with temperature coupling to equilibrate<br>5. turn on pressure coupling and let the system equilibrate<br>6. harvest<br><br>Cheers,<br><br>Tsjerk<br><br><div><span class="gmail_quote">On 11/30/05,
<b class="gmail_sendername">Adriana Pietropaolo</b> <<a href="mailto:adriana@ms.fci.unibo.it">adriana@ms.fci.unibo.it</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Thanks a lot for your help!<br>Now, I had been able to make a reasonable box with 26000 water molecules<br>and my protein.<br>I used grompp and I processed the topology file with 4 tasks.<br>When I run MD simulation, constraining all bonds to equilibrate my water
<br>molecules there's this error:<br>Constraint error in algorithm Lincs at step 0<br> Energies (kJ/mol)<br> Angle Proper Dih. Ryckaert-Bell. LJ-14 Coulomb-14<br> 6.38409e+03 2.55973e+02
4.45790e+03 5.51719e+03 2.38409e+04<br> LJ (SR) LJ (LR) Coulomb (SR) Coulomb (LR) Position Rest.<br> 3.85342e+05 -5.67173e+03 -1.17926e+06 -1.72551e+05 4.23618e+00<br> Potential Kinetic En. Total Energy Temperature Pressure (bar)
<br> -9.31678e+05 2.39317e+05 -6.92360e+05 3.43853e+02 1.93620e+04<br><br>I put in my sistem a pressure of 1.013 bar, but I see a pressure of<br>1.93e+04. The mdrun goes in segmentation fault...<br>I tried to run a NVT too, but nothing.
<br>How can I follow?<br>Thanks in advance,<br>Adriana<br><br><br><br>--<br>_____________________________________________<br>Adriana Pietropaolo,<br>PhD student,<br>dipartimento di Chimica Fisica ed Inorganica,<br>Facolta' di Chimica Industriale
<br>Universita' di Bologna<br>Tel 051/6446992<br>FAX 051/2093690<br>_____________________________________________<br><br><br><br>_______________________________________________<br>gmx-users mailing list<br><a href="mailto:gmx-users@gromacs.org">
gmx-users@gromacs.org</a><br><a href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>Please don't post (un)subscribe requests to the list. Use the<br>www interface or send it to
<a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br></blockquote></div><br><br clear="all"><br>-- <br><br>Tsjerk A. Wassenaar, M.Sc.<br>Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
<br>Dept. of Biophysical Chemistry<br>University of Groningen<br>Nijenborgh 4<br>9747AG Groningen, The Netherlands<br>+31 50 363 4336<br>