Thank you for your suggestions Mark and David. I have read papers you mentioned. Moreover, I also read the Berk Hess's paper in which the NPT & NVT remd was compared (JMB 354/173-183).
Since I have not a high T within my temperature distribution (the highest one is around 320K), there will be no large pressure input. In Berk's paper, it was stated that the fluctuation in volume is negligible in NPT simulation. However, due to the low density value at high T, the energy of the system will be high leading to a decrease in the overlapping of energy distribution as well as the exchange probabilities. I am looking forward to the implementation of NVT within the temperature generator :-) -----Original Message----- From: Mark Abraham <[EMAIL PROTECTED]> To: Discussion list for GROMACS users <gmx-users@gromacs.org> Date: Sun, 24 Feb 2008 13:34:51 +1100 Subject: Re: [gmx-users] problem with exchange probabilities in remd OZGE ENGIN wrote: > Hi all, > > I am performing a remd simulation of a peptide+water system. I have tried > different temperature distributions. I am using an NVT ensemble. My > temperature coupling constant is 0.1 ps. > > The problem is that upon increasing the temperature difference between the > two replicas more than two (290==>294), the exchange probability decreases > sharply, app. to 0.03. Yep. That's normal for decent-sized explicit-solvent REMD. You can choose a lowest temperature spacing that isn't an integer, of course. > I have changed the exchange frequency in order to get a better exchange > probabilities. However, it has not affected the overall exchange > probabilities so much. The frequency is independent of the probability, at least until you get to periods so short that successive attempts are correlated. See Periole and Mark, J Chem Phys 126 014903, and for a counter-view, Sindhikara, Meng and Roitberg J Chem Phys 128 024103. Both frequency and probability affect the exchange acceptance rate, of course. > Is there anybody who has encountered such a situation? Yep. Consider seriously how big a temperature range you might need. There's discussion out there that the increased-sampling effect of the increased temperature range is outweighed by the ability of the replicas to sort themselves as a function of T. See Periole paper above. Thus, there's no need to go to 800K, like you see implicit-solvent REMD achieve. 373K is enough to start denaturing proteins in cooking, after all :-) Mark _______________________________________________ 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 Ozge Engin ================================= Computational Science & Engineering Koc University _______________________________________________ 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
