Thanks Mark. I looked at the link you has sent. However, with pressure coupling I haven't seen such fluctuations for my system. The pressure value is the one obtained at the end of a long NPT simulation - 10^8 steps with dt=10^-4. The rms fluctuations in pressure are small, of the order of 1-0.1 bar.
On Tue, Jun 8, 2010 at 6:34 PM, Mark Abraham <[email protected]>wrote: > ----- Original Message ----- > From: Sai Pooja <[email protected]> > Date: Wednesday, June 9, 2010 8:07 > Subject: [gmx-users] Reduced LJ Units > To: Discussion list for GROMACS users <[email protected]> > > > Hi, > > > I have trouble searching mailing lists so I apologize if this has > already been answered in some query. > > > > If sigma=epsilon=mass=1 is specified in .top file then for specifying > T*=1 in the Thermostat does one need to set ref_t ~ 120 ? > > > > Similarly, to specify ref_p for the Barostat, is there a similar > conversion factor? > > > > How about the values of P reported in bar? How does one convert that to > reduced units? > > Does manual table 2.4 help? > > > > I ask this because I have currently specified ref_t =120 as explained in > the Gromacs manual. However this gives me a pressure value(in bars) which is > much much larger than the one I had expected in reduced units (by a factor > of about 50-60). > > Are you measuring pressure over long enough time? See > http://www.gromacs.org/Documentation/Terminology/Pressure > > Mark > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Quaerendo Invenietis-Seek and you shall discover.
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