Dear Ozge,
lets keep the discussion in the gmx-users list.
Thank you for your quick reply! I used the temperature distribution that was used in your paper: starting from 275.6 to 399.6.
This distribution was chosen to give an exchange ratio of ~0.3 on the system used: a beta-peptide in methanol. Given that you change the system and thus the degrees of freedom you have adapt your temperatures. Their distribution has to be chosen such that the overlap of total potential energy of the system at consecutive temperatures allows exchange. You can tune the separations between the temperatures to vary the exchange rate.
I used the 0.002 ps as time step, but I could not understand what you suggested exactly. You asked the time step for temperature coupling? Is is true? if so, the temperature coupling constant was 0.1.
I was referring to the integration time step, which is the time step you use to integrate the equation of motion that are used to propagate your system in time. If you go to higher temperature the thermal energy is such that the motions of the atoms are increased and you need to decrease the time step of integration to be able to describe the evolution of the system. That might be the reason you see LINCS warnings. Then the fact that you do not use explicit solvent (no viscosity) will increase the motion of the particles (atoms) and may add to the problem described above.
What temperature coupling constant and temperature interval will be appropriate for simulation in vacuum via REMD?
delta=0.001 ps might be enough. You need to make some trials. But again, simulating in vacuo is almost useless, unless you want to show that the sampling is inaccurate.
Have you ever performed REMD in vacuum?
Yes to show that you get erroneous sampling. This is well accepted also there are few papers showing it explicitly. Same thing for the use of implicit solvents but this is more documented in the literature. Look for papers of AE. Garcia and co-workers.
Ozge
XAvier ----------------------------------------------------- XAvier Periole - PhD NMR & Molecular Dynamics Group University of Groningen The Netherlands http://md.chem.rug.nl/~periole ----------------------------------------------------- _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.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