Re: Re: [gmx-users] Nose-hoover T-coupling in REMD
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Re: [gmx-users] Nose-hoover T-coupling in REMD
2010/12/26 ms deviceran...@gmail.com On 25/12/10 02:12, Qin Qiao wrote: Thanks a lot! It says Nose-hoover coupling generates the correct canonical ensemble, and that's the reason why I used it. I wonder whether v-rescale can also get the correct ensemble. Could you tell me? As far as I know v-rescale should generate a correct ensemble. On 25/12/10 12:40, Qin Qiao wrote: I'm not sure, since actually kinetic energy should have fluctuation, and the v-rescaling may suppress the fluctuation.. (PLEASE don't top post!!) Well, the thermostat author, who I happen to know, says it generates the right ensemble. :) I'm not an expert so I can't say if it's true, but if you like you can read the original papers, linked here: http://sites.google.com/site/giovannibussi/Research/algorithms#TOC-A-stochastic-velocity-rescaling-the cheers, m. Thanks a lot! Qin -- Massimo Sandal, Ph.D. http://devicerandom.org -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Nose-hoover T-coupling in REMD
On 25/12/10 02:12, Qin Qiao wrote: Thanks a lot! It says Nose-hoover coupling generates the correct canonical ensemble, and that's the reason why I used it. I wonder whether v-rescale can also get the correct ensemble. Could you tell me? As far as I know v-rescale should generate a correct ensemble. -- Massimo Sandal, Ph.D. http://devicerandom.org -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Nose-hoover T-coupling in REMD
I'm not sure, since actually kinetic energy should have fluctuation, and the v-rescaling may suppress the fluctuation.. 2010/12/25 ms deviceran...@gmail.com On 25/12/10 02:12, Qin Qiao wrote: Thanks a lot! It says Nose-hoover coupling generates the correct canonical ensemble, and that's the reason why I used it. I wonder whether v-rescale can also get the correct ensemble. Could you tell me? As far as I know v-rescale should generate a correct ensemble. -- Massimo Sandal, Ph.D. http://devicerandom.org -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Nose-hoover T-coupling in REMD
On 25/12/2010 1:12 PM, Qin Qiao wrote: Thanks a lot! It says Nose-hoover coupling generates the correct canonical ensemble, and that's the reason why I used it. I wonder whether v-rescale can also get the correct ensemble. Could you tell me? I'm quite curious how to choose the frequency of the T-coupling in REMD. Though it seems the higher the frequency, the more accurate T will be, I wonder whether it will get artifacts for in MD run.. since the warning in Gromacs says tau_t should be 20 times bigger than dt*nsttcouple.. Consider what you mean by accurate T. You actually wish to sample from a given constant temperature ensemble. However that ensemble does not show its average T at every instant - the conserved quantity is not actually temperature. What you want is the right average T and the right fluctuations. Probably you want to read the literature for the T-coupling algorithms to learn more about the details here... Probably I should also too :-) Mark Best, Qin 2010/12/25 David van der Spoel sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se On 12/24/10 6:40 PM, ms wrote: On 24/12/10 12:26, David van der Spoel wrote: I'm not an expert, but isn't Berendsen usually not used because it doesn't give a correct ensemble? I may be partial because I personally know Giovanni Bussi, but it seems from what I've heard that v-rescale is the best choice usually. V-rescale is a good choice. Berendsen not only gives you the wrong ensemble but it also biases the energy distribution to lower energies. Out of curiosity: why is it still supported in GROMACS? Wouldn't lead to less confusion if it is removed? :) It's still useful for equilibration, e.g. gas to liquid conversion. -- David. David van der Spoel, PhD, Professor of Biology Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se sp...@gromacs.org mailto:sp...@gromacs.org http://folding.bmc.uu.se -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Nose-hoover T-coupling in REMD
On 25/12/10 02:12, Qin Qiao wrote: Thanks a lot! It says Nose-hoover coupling generates the correct canonical ensemble, and that's the reason why I used it. I wonder whether v-rescale can also get the correct ensemble. Could you tell me? As far as I know v-rescale should generate a correct ensemble. On 25/12/10 12:40, Qin Qiao wrote: I'm not sure, since actually kinetic energy should have fluctuation, and the v-rescaling may suppress the fluctuation.. (PLEASE don't top post!!) Well, the thermostat author, who I happen to know, says it generates the right ensemble. :) I'm not an expert so I can't say if it's true, but if you like you can read the original papers, linked here: http://sites.google.com/site/giovannibussi/Research/algorithms#TOC-A-stochastic-velocity-rescaling-the cheers, m. -- Massimo Sandal, Ph.D. http://devicerandom.org -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Nose-hoover T-coupling in REMD
On 22/12/2010 5:44 PM, Qin Qiao wrote: Dear all, I posted yesterday but didn't get answer..I guess it's due to my wrong approach to ask. I would like to explain more and hope I would get your help. I'm doing an REMD, and want to have a strong temperature coupling to make sure every replica is at its target temperature. I guess I could do it by setting tau_t small in the Nose-hoover T coupling, but there will come the warning in Gromacs. I maxwarned the warning to proceed, and find the temperature is ok, but I am not sure whether it will introduce some artifacts in the simulation and what kind of artifacts. Could you tell me? Thanks a lot. The temperature coupling algorithms are discussed in the literature, when they were derived (citations in GROMACS manual) and subsequently. I suggest you do your own homework there. The use of REMD is more or less irrelevant to the trade-offs when deciding what temperature coupling scheme to use. Mark Best, Qin 2010/12/21 Qin Qiao qiaoqi...@gmail.com mailto:qiaoqi...@gmail.com Dear all, I wonder what will happen in Nose-hoover coupling when tau_t = dt * nsttcouple, while nsttcouple = nstlist. (I used -maxwarn 1 to ignore the Gromacs warning) I tried this setting, to find the temperature is OK, but I am not sure whether it will introduce some artifacts in the simulation and what kind of artifacts. Could you tell me? Thanks in advance. Best, Qin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Nose-hoover T-coupling in REMD
On 2010-12-24 11.04, Mark Abraham wrote: On 22/12/2010 5:44 PM, Qin Qiao wrote: Dear all, I posted yesterday but didn't get answer..I guess it's due to my wrong approach to ask. I would like to explain more and hope I would get your help. I'm doing an REMD, and want to have a strong temperature coupling to make sure every replica is at its target temperature. I guess I could do it by setting tau_t small in the Nose-hoover T coupling, but there will come the warning in Gromacs. I maxwarned the warning to proceed, and find the temperature is ok, but I am not sure whether it will introduce some artifacts in the simulation and what kind of artifacts. Could you tell me? Thanks a lot. The temperature coupling algorithms are discussed in the literature, when they were derived (citations in GROMACS manual) and subsequently. I suggest you do your own homework there. The use of REMD is more or less irrelevant to the trade-offs when deciding what temperature coupling scheme to use. That is correct, but do not use Berendsen! There is a recent paper from the Garcia group (IIRC) about the effect of Berendsen coupling on REMD sampling. Not good. Mark Best, Qin 2010/12/21 Qin Qiao qiaoqi...@gmail.com mailto:qiaoqi...@gmail.com Dear all, I wonder what will happen in Nose-hoover coupling when tau_t = dt * nsttcouple, while nsttcouple = nstlist. (I used -maxwarn 1 to ignore the Gromacs warning) I tried this setting, to find the temperature is OK, but I am not sure whether it will introduce some artifacts in the simulation and what kind of artifacts. Could you tell me? Thanks in advance. Best, Qin -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Nose-hoover T-coupling in REMD
On 24/12/10 10:36, David van der Spoel wrote: On 2010-12-24 11.04, Mark Abraham wrote: On 22/12/2010 5:44 PM, Qin Qiao wrote: Dear all, I posted yesterday but didn't get answer..I guess it's due to my wrong approach to ask. I would like to explain more and hope I would get your help. I'm doing an REMD, and want to have a strong temperature coupling to make sure every replica is at its target temperature. I guess I could do it by setting tau_t small in the Nose-hoover T coupling, but there will come the warning in Gromacs. I maxwarned the warning to proceed, and find the temperature is ok, but I am not sure whether it will introduce some artifacts in the simulation and what kind of artifacts. Could you tell me? Thanks a lot. The temperature coupling algorithms are discussed in the literature, when they were derived (citations in GROMACS manual) and subsequently. I suggest you do your own homework there. The use of REMD is more or less irrelevant to the trade-offs when deciding what temperature coupling scheme to use. That is correct, but do not use Berendsen! There is a recent paper from the Garcia group (IIRC) about the effect of Berendsen coupling on REMD sampling. Not good. Mark I'm not an expert, but isn't Berendsen usually not used because it doesn't give a correct ensemble? I may be partial because I personally know Giovanni Bussi, but it seems from what I've heard that v-rescale is the best choice usually. -- Massimo Sandal, Ph.D. http://devicerandom.org -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Nose-hoover T-coupling in REMD
On 2010-12-24 13.15, ms wrote: On 24/12/10 10:36, David van der Spoel wrote: On 2010-12-24 11.04, Mark Abraham wrote: On 22/12/2010 5:44 PM, Qin Qiao wrote: Dear all, I posted yesterday but didn't get answer..I guess it's due to my wrong approach to ask. I would like to explain more and hope I would get your help. I'm doing an REMD, and want to have a strong temperature coupling to make sure every replica is at its target temperature. I guess I could do it by setting tau_t small in the Nose-hoover T coupling, but there will come the warning in Gromacs. I maxwarned the warning to proceed, and find the temperature is ok, but I am not sure whether it will introduce some artifacts in the simulation and what kind of artifacts. Could you tell me? Thanks a lot. The temperature coupling algorithms are discussed in the literature, when they were derived (citations in GROMACS manual) and subsequently. I suggest you do your own homework there. The use of REMD is more or less irrelevant to the trade-offs when deciding what temperature coupling scheme to use. That is correct, but do not use Berendsen! There is a recent paper from the Garcia group (IIRC) about the effect of Berendsen coupling on REMD sampling. Not good. Mark I'm not an expert, but isn't Berendsen usually not used because it doesn't give a correct ensemble? I may be partial because I personally know Giovanni Bussi, but it seems from what I've heard that v-rescale is the best choice usually. V-rescale is a good choice. Berendsen not only gives you the wrong ensemble but it also biases the energy distribution to lower energies. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Nose-hoover T-coupling in REMD
On 24/12/10 12:26, David van der Spoel wrote: I'm not an expert, but isn't Berendsen usually not used because it doesn't give a correct ensemble? I may be partial because I personally know Giovanni Bussi, but it seems from what I've heard that v-rescale is the best choice usually. V-rescale is a good choice. Berendsen not only gives you the wrong ensemble but it also biases the energy distribution to lower energies. Out of curiosity: why is it still supported in GROMACS? Wouldn't lead to less confusion if it is removed? :) -- Massimo Sandal, Ph.D. http://devicerandom.org -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Nose-hoover T-coupling in REMD
On 12/24/10 6:40 PM, ms wrote: On 24/12/10 12:26, David van der Spoel wrote: I'm not an expert, but isn't Berendsen usually not used because it doesn't give a correct ensemble? I may be partial because I personally know Giovanni Bussi, but it seems from what I've heard that v-rescale is the best choice usually. V-rescale is a good choice. Berendsen not only gives you the wrong ensemble but it also biases the energy distribution to lower energies. Out of curiosity: why is it still supported in GROMACS? Wouldn't lead to less confusion if it is removed? :) It's still useful for equilibration, e.g. gas to liquid conversion. -- David. David van der Spoel, PhD, Professor of Biology Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 sp...@xray.bmc.uu.sesp...@gromacs.org http://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Nose-hoover T-coupling in REMD
Thanks a lot! It says Nose-hoover coupling generates the correct canonical ensemble, and that's the reason why I used it. I wonder whether v-rescale can also get the correct ensemble. Could you tell me? I'm quite curious how to choose the frequency of the T-coupling in REMD. Though it seems the higher the frequency, the more accurate T will be, I wonder whether it will get artifacts for in MD run.. since the warning in Gromacs says tau_t should be 20 times bigger than dt*nsttcouple.. Best, Qin 2010/12/25 David van der Spoel sp...@xray.bmc.uu.se On 12/24/10 6:40 PM, ms wrote: On 24/12/10 12:26, David van der Spoel wrote: I'm not an expert, but isn't Berendsen usually not used because it doesn't give a correct ensemble? I may be partial because I personally know Giovanni Bussi, but it seems from what I've heard that v-rescale is the best choice usually. V-rescale is a good choice. Berendsen not only gives you the wrong ensemble but it also biases the energy distribution to lower energies. Out of curiosity: why is it still supported in GROMACS? Wouldn't lead to less confusion if it is removed? :) It's still useful for equilibration, e.g. gas to liquid conversion. -- David. David van der Spoel, PhD, Professor of Biology Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 sp...@xray.bmc.uu.sesp...@gromacs.org http://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
