What I meant by using a tau_t of 3000 ps is to effectively turn off the
thermostat for water. What I want to do is let the wall thermostat to
take care of the temperature control (if the water temperature rises,
the heat are supposed to get out through the wall thermostat). But
somehow this does not happen.<br>
<br>
Nick<br><br><div><span class="gmail_quote">On 1/12/06, <b class="gmail_sendername">Simple</b> <<a href="mailto:qsb@nlbmol.ibp.ac.cn">qsb@nlbmol.ibp.ac.cn</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;">
Nickle Fan writed£º<br>> Dear Gromacs users:<br>><br>> I am having a rather strange problem in one of my simulation. The system<br>> consists of 2000 water molecules embedded between two walls. The wall atoms<br>
> are position restrainted (force constant: 5000).<br>><br>> The system is first equiliburated under NVT (Berendsen thermostat, tau_t =<br>> 0.1ps, Tsystem = 300K) for a while. Then I coupled the wall atoms to 300K
<br>> (tau_t = 0.1 ps), and water to 300K (tau_t = 3000 ps). I found that during<br>I found you used (tau_t = 3000 ps) for water, I don't know why you use<br>different tau_t for wall and water.But I think, under your setting, the
<br>temperature will only couple at 3000 ps interval. So in a 100ps simulation,<br>the temperature of water would never adjust,Then the increasing of temp seem<br>reasonable.<br>I'm not familiar with this problem.I only notice the strange setting, maybe
<br>there are other opinions,<br>> a 100ps simulation, the temperature of water rise continuously to 400K!<br>> (the wall atoms are OK though). I tried to disable water temperature<br>> coupling by set tau_t = 0 for water, but it does not help.
<br>><br>> I tried NVE simulation from the same initial configuration, and it appears<br>> that the temperature of water during the first 50 ps is about 300K. So we<br>> can rule out the possibility of bad local contact in the system. Then what
<br>> could possibly goes wrong with the system?<br>><br>> I am using PME (4th order), vdw-type = Shift, rvdw-switch = 0, rvdw =<br>> 1.1, rlist = 1.2. Time step is 1fs.<br>><br>> Any help would be greatly appreciated.
<br>><br>> Nick Fan<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">
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</a>.<br></blockquote></div><br>