Dear Mark,<br><br>Thanks for your help, I followed you instruction, and I can get stable temperature after I remove the temperature coupling. In this case I used the flexible spc itp file. However if I use a rigid spc.itp, after remveing the temperature coupling, the system temperature is shooting up from 300K to thousands degree, the total energy is going up also instead of fluctuating. I attached both the itp files and grompp.mdp files. Let me know what could be wrong. It is really wired to me. <br><br>Thanks,<br><br>Cherry<br><br><b><i>Mark Abraham <Mark.Abraham@anu.edu.au></i></b> wrote:<blockquote class="replbq" style="border-left: 2px solid rgb(16, 16, 255); margin-left: 5px; padding-left: 5px;"> Cherry Y. Yates wrote:<br>> Dear GROMACS developers,<br>> <br>> I would like to do a SPC-water simulation without temperature coupling. <br>> I set tcouple to 300K and did Berenderson T-coupling first for 400 ps to <br>> equilibrate the system. Then
I copy confout.gro to conf.gro, set tcoupl <br>> to no. However the Temperature of the later similation jumped from 300K <br>> to 520K immediately and fluctuate around 520K instead of 300K. I wonder <br>> (1) what could be wrong? <br><br>The .mdp file you attached has gen_vel = yes, which if used for the <br>second calculation will lead to regeneration of velocities and might <br>explain this behaviour. You will need to supply .trr and .edr files to <br>grompp for this second stage, of course.<br><br>> (2) how can I do a single simulation in which <br>> first 400 ps using some temperature coupling scheme to equilibrate the <br>> system, then do 100 ps without temperature coupling? I attached the <br>> grompp.mdp file.<br><br>You can't do this in a single simulation, however it's straightforward <br>to prepare your .mdp files in advance and have a script run a<br><br>grompp -f -c -p -o<br>mdrun -s<br>grompp -f -c -p -o -e -t<br>mdrun -s<br><br>sequence
to deal with what you want to do.<br><br>Mark<br>_______________________________________________<br>gmx-users mailing list gmx-users@gromacs.org<br>http://www.gromacs.org/mailman/listinfo/gmx-users<br>Please don't post (un)subscribe requests to the list. Use the <br>www interface or send it to gmx-users-request@gromacs.org.<br>Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br></blockquote><br><p> 
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