Re: [gmx-users] Acetone parameters and transferability question
Hello Justin, and thank you for your reply. Yes, the diffusion constant with the ATB acetone (code name _LVN) was overestimated in a variety of molar ratios (used SPC water), but also, I am not able to reproduce acetone's experimental density correctly (result was around 830 rather than 791 kg/m^3) When building the acetone-solvation boxes, I have followed the guides from Gromacs. Another fact is that the second acetone model ATB has, (code name AON, a united atom model for the 53a5ff) is immiscible with water, possibly due to the very low charge in the C=O molecules. How can I be certain that the acetone model I use is OK? I am trying to be as careful as possible but really need an expert's advice on which molecule to use. Again thank you for your time, Ioanna This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please send it back to me, and immediately delete it. Please do not use, copy or disclose the information contained in this message or in any attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham. This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system, you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Gromacs API AnalysisData Class
On 2014-10-12 03:50, Yunlong Liu wrote: Hi, I am developing some personal trajectory analysis code with Gromacs API. I have a question on using the AnalysisData class. I would like to have access to the data stored in the AnalysisData object after running a single pass over all the frames in the trajectory. I don't know how to do it and where to find the stored data. For example, I extract a position vector from each frame and use setPoint to set it into AnalysisDataHandle in the function analysisFrame. After my program run through all the frames, how can I access those position vectors stored in my AnalysisData object. Thank you. Yunlong Please repost your question on the gmx-developer mailing list. -- 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 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Acetone parameters and transferability question
830 versus 791 kg/m^3 is not that terrible discrepancy in the case of united-atom models and other details from below... Acetone falls within the group of those small molecules, which are easy to (re)parameterize. Dr. Vitaly V. Chaban Виталий Витальевич ЧАБАН On Sun, Oct 12, 2014 at 11:38 AM, Ioanna Styliari wrote: > Hello Justin, and thank you for your reply. > > Yes, the diffusion constant with the ATB acetone (code name _LVN) was > overestimated in a variety of molar ratios (used SPC water), but also, I am > not able to reproduce acetone's experimental density correctly (result was > around 830 rather than 791 kg/m^3) > When building the acetone-solvation boxes, I have followed the guides from > Gromacs. > Another fact is that the second acetone model ATB has, (code name AON, a > united atom model for the 53a5ff) is immiscible with water, possibly due to > the very low charge in the C=O molecules. > How can I be certain that the acetone model I use is OK? I am trying to be as > careful as possible but really need an expert's advice on which molecule to > use. > > Again thank you for your time, > > Ioanna > > This message and any attachment are intended solely for the addressee and may > contain confidential information. If you have received this message in error, > please send it back to me, and immediately delete it. Please do not use, > copy or disclose the information contained in this message or in any > attachment. Any views or opinions expressed by the author of this email do > not necessarily reflect the views of the University of Nottingham. > > > > This message has been checked for viruses but the contents of an attachment > > may still contain software viruses which could damage your computer system, > you are advised to perform your own checks. Email communications with the > University of Nottingham may be monitored as permitted by UK legislation. > > > > > > > > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Use NVT to mimic NVE
Firstly, what are the possible errors/artifacts caused by masking "the energy leakage problem with the thermostat" in this case? Secondly, are there any other mdp setting that I can try to make the mixed precision gromacs NVE run have conserved energy over 100 ns ? (and... is it because of some errors that I made in my systems that make the NVE run not conserved in energy?) The NVE has the following statistics. Statistics over 2747281 steps [ 0. through 1373.6400 ps ], 4 data sets All statistics are over 274729 points Energy Average Err.Est. RMSD Tot-Drift --- Disper. corr. -3961.13 0 0 2.60178e-09 (kJ/mol) Total Energy-309939160 337.76478.828 (kJ/mol) Temperature 300.292 0.241.49289 0.631428 (K) Pressure -64.54094.7148.77925.1326 (bar) -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Use NVT to mimic NVE
The artifacts are caused by energy leakage. Thermostatting does not solve them. The problem exists, but you do not see it clearly with thermostat. For instance, I have an example where a liquid droplet in vacuum is not stable due to bad energy conservation. Some particles just sporadically fly away over the course of the simulation. NVE generally does not like constraints. If I remember correctly from the previous messages, you use constraints. Novel performance improvements in gromacs (accumulated after 4.0 and especially after 4.5) sometimes compromise accuracy, though it is a long discussion itself. What about downgrading to gmx 4.0 or gmx 3.3, after all? The very last time I used gromacs for NVE simulation was in 2009. I guess I used gmx 3.3.3 (but maybe 4.0.x). There were no problems for sure. I would also give a try to some very simple system (e.g. liquid argon) to observe what happens to total energy. Good luck with troubleshooting! Dr. Vitaly V. Chaban Виталий Витальевич ЧАБАН On Sun, Oct 12, 2014 at 4:53 PM, Johnny Lu wrote: > Firstly, what are the possible errors/artifacts caused by masking "the > energy leakage problem with the thermostat" in this case? > > Secondly, are there any other mdp setting that I can try to make the mixed > precision gromacs NVE run have conserved energy over 100 ns ? (and... is it > because of some errors that I made in my systems that make the NVE run not > conserved in energy?) > > The NVE has the following statistics. > > Statistics over 2747281 steps [ 0. through 1373.6400 ps ], 4 data sets > All statistics are over 274729 points > > Energy Average Err.Est. RMSD Tot-Drift > --- > Disper. corr. -3961.13 0 0 2.60178e-09 > (kJ/mol) > Total Energy-309939160 337.76478.828 > (kJ/mol) > Temperature 300.292 0.241.49289 0.631428 (K) > Pressure -64.54094.7148.77925.1326 (bar) > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Acetone parameters and transferability question
On 10/12/14 5:38 AM, Ioanna Styliari wrote: Hello Justin, and thank you for your reply. Yes, the diffusion constant with the ATB acetone (code name _LVN) was overestimated in a variety of molar ratios (used SPC water), but also, I am not able to reproduce acetone's experimental density correctly (result was around 830 rather than 791 kg/m^3) When building the acetone-solvation boxes, A 5% error is actually rather good. I have followed the guides from Gromacs. Another fact is that the second acetone model ATB has, (code name AON, a united atom model for the 53a5ff) is immiscible with water, possibly due to the very low charge in the C=O molecules. How can I be certain that the acetone model I use is OK? I am The 53A5 parameters are for simulations in cyclohexane, not water, hence the insolubility is to be expected. trying to be as careful as possible but really need an expert's advice on which molecule to use. If the density is only off by 5%, it should be reasonably easy to tweak the parameters. To be in line with the existing force field, target data should also include heat of vaporization and solvation free energy. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Use NVT to mimic NVE
I believe the major problem with energy losses is that your system never achieves equilibrium. Thus, all the simulated properties are not what they need to be... Dr. Vitaly V. Chaban Виталий Витальевич ЧАБАН On Sun, Oct 12, 2014 at 5:31 PM, Dr. Vitaly Chaban wrote: > The artifacts are caused by energy leakage. Thermostatting does not > solve them. The problem exists, but you do not see it clearly with > thermostat. For instance, I have an example where a liquid droplet in > vacuum is not stable due to bad energy conservation. Some particles > just sporadically fly away over the course of the simulation. > > NVE generally does not like constraints. If I remember correctly from > the previous messages, you use constraints. Novel performance > improvements in gromacs (accumulated after 4.0 and especially after > 4.5) sometimes compromise accuracy, though it is a long discussion > itself. What about downgrading to gmx 4.0 or gmx 3.3, after all? The > very last time I used gromacs for NVE simulation was in 2009. I guess > I used gmx 3.3.3 (but maybe 4.0.x). There were no problems for sure. > > I would also give a try to some very simple system (e.g. liquid argon) > to observe what happens to total energy. > > Good luck with troubleshooting! > > > Dr. Vitaly V. Chaban > > Виталий Витальевич ЧАБАН > > > On Sun, Oct 12, 2014 at 4:53 PM, Johnny Lu wrote: >> Firstly, what are the possible errors/artifacts caused by masking "the >> energy leakage problem with the thermostat" in this case? >> >> Secondly, are there any other mdp setting that I can try to make the mixed >> precision gromacs NVE run have conserved energy over 100 ns ? (and... is it >> because of some errors that I made in my systems that make the NVE run not >> conserved in energy?) >> >> The NVE has the following statistics. >> >> Statistics over 2747281 steps [ 0. through 1373.6400 ps ], 4 data sets >> All statistics are over 274729 points >> >> Energy Average Err.Est. RMSD Tot-Drift >> --- >> Disper. corr. -3961.13 0 0 2.60178e-09 >> (kJ/mol) >> Total Energy-309939160 337.76478.828 >> (kJ/mol) >> Temperature 300.292 0.241.49289 0.631428 (K) >> Pressure -64.54094.7148.77925.1326 (bar) >> -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a >> mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Use NVT to mimic NVE
Why non-equilibrium can cause lost of total energy in NVE simulation? (baring the case that the non-equilibrium causes very large values that causes over flow / getting out of the stable range of algorithms of gromacs). A closed system should have constant energy, regardless of whether it is at equilibrium. I guess people use the word "converge" instead of equilibrium in molecular dynamics simulation of protein, possibly because the simulation may never reach equilibrium with current computing power. http://pubs.rsc.org/en/content/articlepdf/2012/cp/c2cp23961b I may try older version of gromacs and/or not using constraint, after checking the bug list and performance. I had never thought about that route. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Use NVT to mimic NVE
On 2014-10-12 17:31, Dr. Vitaly Chaban wrote: The artifacts are caused by energy leakage. Thermostatting does not solve them. The problem exists, but you do not see it clearly with thermostat. For instance, I have an example where a liquid droplet in vacuum is not stable due to bad energy conservation. Some particles just sporadically fly away over the course of the simulation. We have run 3 microsecond simulations of water droplets in vacuum with perfect energy conservation, double precision, no cut-off and SETTLE. With constraint solvers it is indeed close to impossible to get real energy conservation. Turning off the constraints and using a time step <= 0.5 fs might work somewhat better with mixed precision, and these degrees of freedom may be important for energy transfer too. NVE generally does not like constraints. If I remember correctly from the previous messages, you use constraints. Novel performance improvements in gromacs (accumulated after 4.0 and especially after 4.5) sometimes compromise accuracy, though it is a long discussion itself. What about downgrading to gmx 4.0 or gmx 3.3, after all? The very last time I used gromacs for NVE simulation was in 2009. I guess I used gmx 3.3.3 (but maybe 4.0.x). There were no problems for sure. I would also give a try to some very simple system (e.g. liquid argon) to observe what happens to total energy. Good luck with troubleshooting! Dr. Vitaly V. Chaban Виталий Витальевич ЧАБАН On Sun, Oct 12, 2014 at 4:53 PM, Johnny Lu wrote: Firstly, what are the possible errors/artifacts caused by masking "the energy leakage problem with the thermostat" in this case? Secondly, are there any other mdp setting that I can try to make the mixed precision gromacs NVE run have conserved energy over 100 ns ? (and... is it because of some errors that I made in my systems that make the NVE run not conserved in energy?) The NVE has the following statistics. Statistics over 2747281 steps [ 0. through 1373.6400 ps ], 4 data sets All statistics are over 274729 points Energy Average Err.Est. RMSD Tot-Drift --- Disper. corr. -3961.13 0 0 2.60178e-09 (kJ/mol) Total Energy-309939160 337.76478.828 (kJ/mol) Temperature 300.292 0.241.49289 0.631428 (K) Pressure -64.54094.7148.77925.1326 (bar) -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- 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 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Use NVT to mimic NVE
The point was that if the energy leaves the system, then the system is never in equilibrium. Not vice versa, please. Dr. Vitaly V. Chaban Виталий Витальевич ЧАБАН On Sun, Oct 12, 2014 at 7:20 PM, Johnny Lu wrote: > Why non-equilibrium can cause lost of total energy in NVE simulation? > (baring the case that the non-equilibrium causes very large values that > causes over flow / getting out of the stable range of algorithms of > gromacs). > > A closed system should have constant energy, regardless of whether it is at > equilibrium. > > I guess people use the word "converge" instead of equilibrium in molecular > dynamics simulation of protein, possibly because the simulation may never > reach equilibrium with current computing power. > http://pubs.rsc.org/en/content/articlepdf/2012/cp/c2cp23961b > > I may try older version of gromacs and/or not using constraint, after > checking the bug list and performance. I had never thought about that route. > > > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Use NVT to mimic NVE
> The point was that if the energy leaves the system, then the system is never in equilibrium. Not vice versa, please. This is incorrect logic. f there are errors in the integrator, then F=gradient of the potential is not true. If that is not true, energy is not conserved, and energy can leave or enter the system. On Sun, Oct 12, 2014 at 1:58 PM, Dr. Vitaly Chaban wrote: > The point was that if the energy leaves the system, then the system is > never in equilibrium. Not vice versa, please. > > > > Dr. Vitaly V. Chaban > > Виталий Витальевич ЧАБАН > > > On Sun, Oct 12, 2014 at 7:20 PM, Johnny Lu wrote: > > Why non-equilibrium can cause lost of total energy in NVE simulation? > > (baring the case that the non-equilibrium causes very large values that > > causes over flow / getting out of the stable range of algorithms of > > gromacs). > > > > A closed system should have constant energy, regardless of whether it is > at > > equilibrium. > > > > I guess people use the word "converge" instead of equilibrium in > molecular > > dynamics simulation of protein, possibly because the simulation may never > > reach equilibrium with current computing power. > > http://pubs.rsc.org/en/content/articlepdf/2012/cp/c2cp23961b > > > > I may try older version of gromacs and/or not using constraint, after > > checking the bug list and performance. I had never thought about that > route. > > > > > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Use NVT to mimic NVE
Sorry that I misunderstood your post. Can compensating energy lost caused by numerical error with thermostat cause error in the probability distribution of thermodynamic variables and distribution of conformations? Below is just a guess. I don't understand the fluctuation dissipation theorem enough at this point. I would guess so.. unless the fluctuation of the velocity of the atom doesn't follow maxwell-Boltzmann distribution (I guess that can happen in a crystal made of harmonic oscillator of a single frequency, or if some part of the protein has low degree of freedom. This is a flaw found in nose-hover thermostats.) Otherwise, some thermostats already try to provide the correct fluctuation, so that the distribution of thermodynamic variables is correct (as in fluctuation-dissipation theorem). If we use thermostats, the thermostats will correct the energy drop/raise caused by numerical error (which acts as a fluctuating source/sink that may not even follow the normal distribution), without causing additional artifacts. Regardless, thermostats causes artifacts, especially in dynamics and rates. On Sun, Oct 12, 2014 at 2:07 PM, Michael Shirts wrote: > > The point was that if the energy leaves the system, then the system > is never in equilibrium. Not vice versa, please. > > This is incorrect logic. f there are errors in the integrator, then > F=gradient of the potential is not true. If that is not true, energy is not > conserved, and energy can leave or enter the system. > > > On Sun, Oct 12, 2014 at 1:58 PM, Dr. Vitaly Chaban > wrote: > > > The point was that if the energy leaves the system, then the system is > > never in equilibrium. Not vice versa, please. > > > > > > > > Dr. Vitaly V. Chaban > > > > Виталий Витальевич ЧАБАН > > > > > > On Sun, Oct 12, 2014 at 7:20 PM, Johnny Lu > wrote: > > > Why non-equilibrium can cause lost of total energy in NVE simulation? > > > (baring the case that the non-equilibrium causes very large values that > > > causes over flow / getting out of the stable range of algorithms of > > > gromacs). > > > > > > A closed system should have constant energy, regardless of whether it > is > > at > > > equilibrium. > > > > > > I guess people use the word "converge" instead of equilibrium in > > molecular > > > dynamics simulation of protein, possibly because the simulation may > never > > > reach equilibrium with current computing power. > > > http://pubs.rsc.org/en/content/articlepdf/2012/cp/c2cp23961b > > > > > > I may try older version of gromacs and/or not using constraint, after > > > checking the bug list and performance. I had never thought about that > > route. > > > > > > > > > > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Acetone parameters and transferability question
Thank you both very much for your very useful comments! Just to clarify, when you say "tweak the parameters", would just an investigation of the change of the charges be sufficient? Ioanna This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please send it back to me, and immediately delete it. Please do not use, copy or disclose the information contained in this message or in any attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham. This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system, you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Use NVT to mimic NVE
oh, i still mix up things. the numerical error might act as dissipation. On Sun, Oct 12, 2014 at 3:01 PM, Johnny Lu wrote: > Sorry that I misunderstood your post. > > Can compensating energy lost caused by numerical error with thermostat > cause error in the probability distribution of thermodynamic variables and > distribution of conformations? > > Below is just a guess. I don't understand the fluctuation dissipation > theorem enough at this point. > > I would guess so.. unless the fluctuation of the velocity of the atom > doesn't follow maxwell-Boltzmann distribution (I guess that can happen in a > crystal made of harmonic oscillator of a single frequency, or if some part > of the protein has low degree of freedom. This is a flaw found in > nose-hover thermostats.) > > Otherwise, some thermostats already try to provide the correct > fluctuation, so that the distribution of thermodynamic variables is correct > (as in fluctuation-dissipation theorem). If we use thermostats, the > thermostats will correct the energy drop/raise caused by numerical error > (which acts as a fluctuating source/sink that may not even follow the > normal distribution), without causing additional artifacts. > > Regardless, thermostats causes artifacts, especially in dynamics and rates. > > On Sun, Oct 12, 2014 at 2:07 PM, Michael Shirts > wrote: > >> > The point was that if the energy leaves the system, then the system >> is never in equilibrium. Not vice versa, please. >> >> This is incorrect logic. f there are errors in the integrator, then >> F=gradient of the potential is not true. If that is not true, energy is >> not >> conserved, and energy can leave or enter the system. >> >> >> On Sun, Oct 12, 2014 at 1:58 PM, Dr. Vitaly Chaban >> wrote: >> >> > The point was that if the energy leaves the system, then the system is >> > never in equilibrium. Not vice versa, please. >> > >> > >> > >> > Dr. Vitaly V. Chaban >> > >> > Виталий Витальевич ЧАБАН >> > >> > >> > On Sun, Oct 12, 2014 at 7:20 PM, Johnny Lu >> wrote: >> > > Why non-equilibrium can cause lost of total energy in NVE simulation? >> > > (baring the case that the non-equilibrium causes very large values >> that >> > > causes over flow / getting out of the stable range of algorithms of >> > > gromacs). >> > > >> > > A closed system should have constant energy, regardless of whether it >> is >> > at >> > > equilibrium. >> > > >> > > I guess people use the word "converge" instead of equilibrium in >> > molecular >> > > dynamics simulation of protein, possibly because the simulation may >> never >> > > reach equilibrium with current computing power. >> > > http://pubs.rsc.org/en/content/articlepdf/2012/cp/c2cp23961b >> > > >> > > I may try older version of gromacs and/or not using constraint, after >> > > checking the bug list and performance. I had never thought about that >> > route. >> > > >> > > >> > > >> > -- >> > Gromacs Users mailing list >> > >> > * Please search the archive at >> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> > posting! >> > >> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > >> > * For (un)subscribe requests visit >> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> > send a mail to gmx-users-requ...@gromacs.org. >> > >> -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-requ...@gromacs.org. >> > > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Use NVT to mimic NVE
> If we use thermostats, the thermostats will correct the energy drop/raise caused by numerical error (which acts as a fluctuating source/sink that may not even follow the normal distribution), without causing additional artifacts. Thermostats correct SOME of the artifacts. It is not always clear which ones. > Regardless, thermostats causes artifacts, especially in dynamics and rates. In SOME cases it may be negligible. In others, not. It is very hard to say. See our paper linked before http://pubs.acs.org/doi/abs/10.1021/ct400109a "Effects of Temperature Control Algorithms on Transport Properties and Kinetics in Molecular Dynamics Simulations" which covers most short-time scale effects. Whether the thermostats that do not affect short time scale properties to any noticable degree still affect long-time scale properties through some sort of error accumulation is not known, nor which properties they might affect. On Sun, Oct 12, 2014 at 3:07 PM, Johnny Lu wrote: > oh, i still mix up things. the numerical error might act as dissipation. > > On Sun, Oct 12, 2014 at 3:01 PM, Johnny Lu wrote: > > > Sorry that I misunderstood your post. > > > > Can compensating energy lost caused by numerical error with thermostat > > cause error in the probability distribution of thermodynamic variables > and > > distribution of conformations? > > > > Below is just a guess. I don't understand the fluctuation dissipation > > theorem enough at this point. > > > > I would guess so.. unless the fluctuation of the velocity of the atom > > doesn't follow maxwell-Boltzmann distribution (I guess that can happen > in a > > crystal made of harmonic oscillator of a single frequency, or if some > part > > of the protein has low degree of freedom. This is a flaw found in > > nose-hover thermostats.) > > > > Otherwise, some thermostats already try to provide the correct > > fluctuation, so that the distribution of thermodynamic variables is > correct > > (as in fluctuation-dissipation theorem). If we use thermostats, the > > thermostats will correct the energy drop/raise caused by numerical error > > (which acts as a fluctuating source/sink that may not even follow the > > normal distribution), without causing additional artifacts. > > > > Regardless, thermostats causes artifacts, especially in dynamics and > rates. > > > > On Sun, Oct 12, 2014 at 2:07 PM, Michael Shirts > > wrote: > > > >> > The point was that if the energy leaves the system, then the system > >> is never in equilibrium. Not vice versa, please. > >> > >> This is incorrect logic. f there are errors in the integrator, then > >> F=gradient of the potential is not true. If that is not true, energy is > >> not > >> conserved, and energy can leave or enter the system. > >> > >> > >> On Sun, Oct 12, 2014 at 1:58 PM, Dr. Vitaly Chaban > >> wrote: > >> > >> > The point was that if the energy leaves the system, then the system is > >> > never in equilibrium. Not vice versa, please. > >> > > >> > > >> > > >> > Dr. Vitaly V. Chaban > >> > > >> > Виталий Витальевич ЧАБАН > >> > > >> > > >> > On Sun, Oct 12, 2014 at 7:20 PM, Johnny Lu > >> wrote: > >> > > Why non-equilibrium can cause lost of total energy in NVE > simulation? > >> > > (baring the case that the non-equilibrium causes very large values > >> that > >> > > causes over flow / getting out of the stable range of algorithms of > >> > > gromacs). > >> > > > >> > > A closed system should have constant energy, regardless of whether > it > >> is > >> > at > >> > > equilibrium. > >> > > > >> > > I guess people use the word "converge" instead of equilibrium in > >> > molecular > >> > > dynamics simulation of protein, possibly because the simulation may > >> never > >> > > reach equilibrium with current computing power. > >> > > http://pubs.rsc.org/en/content/articlepdf/2012/cp/c2cp23961b > >> > > > >> > > I may try older version of gromacs and/or not using constraint, > after > >> > > checking the bug list and performance. I had never thought about > that > >> > route. > >> > > > >> > > > >> > > > >> > -- > >> > Gromacs Users mailing list > >> > > >> > * Please search the archive at > >> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > >> > posting! > >> > > >> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >> > > >> > * For (un)subscribe requests visit > >> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > >> > send a mail to gmx-users-requ...@gromacs.org. > >> > > >> -- > >> Gromacs Users mailing list > >> > >> * Please search the archive at > >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > >> posting! > >> > >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >> > >> * For (un)subscribe requests visit > >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > >> send a mail to gmx-users-requ...@gromacs.org. > >> > > > > > -- > Gromacs Users mailing list > > * Please search the archive at >
Re: [gmx-users] Use NVT to mimic NVE
Thank you for pointing me to that paper. I took a quick look of it yesterday. Would the results in the paper stay the same, if the side chain rotations of a protein is investigated? On Sun, Oct 12, 2014 at 3:30 PM, Michael Shirts wrote: > > If we use thermostats, the thermostats will correct the energy drop/raise > caused by numerical error (which acts as a fluctuating source/sink that may > not even follow the normal distribution), without causing additional > artifacts. > > Thermostats correct SOME of the artifacts. It is not always clear which > ones. > > > Regardless, thermostats causes artifacts, especially in dynamics and > rates. > > In SOME cases it may be negligible. In others, not. It is very hard to > say. > > See our paper linked before http://pubs.acs.org/doi/abs/10.1021/ct400109a > "Effects of Temperature Control Algorithms on Transport Properties and > Kinetics in Molecular Dynamics Simulations" which covers most short-time > scale effects. > > Whether the thermostats that do not affect short time scale properties to > any noticable degree still affect long-time scale properties through some > sort of error accumulation is not known, nor which properties they might > affect. > > > On Sun, Oct 12, 2014 at 3:07 PM, Johnny Lu wrote: > > > oh, i still mix up things. the numerical error might act as dissipation. > > > > On Sun, Oct 12, 2014 at 3:01 PM, Johnny Lu > wrote: > > > > > Sorry that I misunderstood your post. > > > > > > Can compensating energy lost caused by numerical error with thermostat > > > cause error in the probability distribution of thermodynamic variables > > and > > > distribution of conformations? > > > > > > Below is just a guess. I don't understand the fluctuation dissipation > > > theorem enough at this point. > > > > > > I would guess so.. unless the fluctuation of the velocity of the atom > > > doesn't follow maxwell-Boltzmann distribution (I guess that can happen > > in a > > > crystal made of harmonic oscillator of a single frequency, or if some > > part > > > of the protein has low degree of freedom. This is a flaw found in > > > nose-hover thermostats.) > > > > > > Otherwise, some thermostats already try to provide the correct > > > fluctuation, so that the distribution of thermodynamic variables is > > correct > > > (as in fluctuation-dissipation theorem). If we use thermostats, the > > > thermostats will correct the energy drop/raise caused by numerical > error > > > (which acts as a fluctuating source/sink that may not even follow the > > > normal distribution), without causing additional artifacts. > > > > > > Regardless, thermostats causes artifacts, especially in dynamics and > > rates. > > > > > > On Sun, Oct 12, 2014 at 2:07 PM, Michael Shirts > > > wrote: > > > > > >> > The point was that if the energy leaves the system, then the system > > >> is never in equilibrium. Not vice versa, please. > > >> > > >> This is incorrect logic. f there are errors in the integrator, then > > >> F=gradient of the potential is not true. If that is not true, energy > is > > >> not > > >> conserved, and energy can leave or enter the system. > > >> > > >> > > >> On Sun, Oct 12, 2014 at 1:58 PM, Dr. Vitaly Chaban < > vvcha...@gmail.com> > > >> wrote: > > >> > > >> > The point was that if the energy leaves the system, then the system > is > > >> > never in equilibrium. Not vice versa, please. > > >> > > > >> > > > >> > > > >> > Dr. Vitaly V. Chaban > > >> > > > >> > Виталий Витальевич ЧАБАН > > >> > > > >> > > > >> > On Sun, Oct 12, 2014 at 7:20 PM, Johnny Lu > > >> wrote: > > >> > > Why non-equilibrium can cause lost of total energy in NVE > > simulation? > > >> > > (baring the case that the non-equilibrium causes very large values > > >> that > > >> > > causes over flow / getting out of the stable range of algorithms > of > > >> > > gromacs). > > >> > > > > >> > > A closed system should have constant energy, regardless of whether > > it > > >> is > > >> > at > > >> > > equilibrium. > > >> > > > > >> > > I guess people use the word "converge" instead of equilibrium in > > >> > molecular > > >> > > dynamics simulation of protein, possibly because the simulation > may > > >> never > > >> > > reach equilibrium with current computing power. > > >> > > http://pubs.rsc.org/en/content/articlepdf/2012/cp/c2cp23961b > > >> > > > > >> > > I may try older version of gromacs and/or not using constraint, > > after > > >> > > checking the bug list and performance. I had never thought about > > that > > >> > route. > > >> > > > > >> > > > > >> > > > > >> > -- > > >> > Gromacs Users mailing list > > >> > > > >> > * Please search the archive at > > >> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > >> > posting! > > >> > > > >> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > >> > > > >> > * For (un)subscribe requests visit > > >> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > or > > >> > send a mail to gmx-users-r
Re: [gmx-users] Use NVT to mimic NVE
I am not quite in the business of folding/unfolding protein. On Sun, Oct 12, 2014 at 4:07 PM, Johnny Lu wrote: > Thank you for pointing me to that paper. I took a quick look of it > yesterday. > Would the results in the paper stay the same, if the side chain rotations > of a protein is investigated? > > On Sun, Oct 12, 2014 at 3:30 PM, Michael Shirts > wrote: > >> > If we use thermostats, the thermostats will correct the energy >> drop/raise >> caused by numerical error (which acts as a fluctuating source/sink that >> may >> not even follow the normal distribution), without causing additional >> artifacts. >> >> Thermostats correct SOME of the artifacts. It is not always clear which >> ones. >> >> > Regardless, thermostats causes artifacts, especially in dynamics and >> rates. >> >> In SOME cases it may be negligible. In others, not. It is very hard to >> say. >> >> See our paper linked before http://pubs.acs.org/doi/abs/10.1021/ct400109a >> "Effects of Temperature Control Algorithms on Transport Properties and >> Kinetics in Molecular Dynamics Simulations" which covers most short-time >> scale effects. >> >> Whether the thermostats that do not affect short time scale properties to >> any noticable degree still affect long-time scale properties through some >> sort of error accumulation is not known, nor which properties they might >> affect. >> >> >> On Sun, Oct 12, 2014 at 3:07 PM, Johnny Lu >> wrote: >> >> > oh, i still mix up things. the numerical error might act as dissipation. >> > >> > On Sun, Oct 12, 2014 at 3:01 PM, Johnny Lu >> wrote: >> > >> > > Sorry that I misunderstood your post. >> > > >> > > Can compensating energy lost caused by numerical error with thermostat >> > > cause error in the probability distribution of thermodynamic variables >> > and >> > > distribution of conformations? >> > > >> > > Below is just a guess. I don't understand the fluctuation dissipation >> > > theorem enough at this point. >> > > >> > > I would guess so.. unless the fluctuation of the velocity of the atom >> > > doesn't follow maxwell-Boltzmann distribution (I guess that can happen >> > in a >> > > crystal made of harmonic oscillator of a single frequency, or if some >> > part >> > > of the protein has low degree of freedom. This is a flaw found in >> > > nose-hover thermostats.) >> > > >> > > Otherwise, some thermostats already try to provide the correct >> > > fluctuation, so that the distribution of thermodynamic variables is >> > correct >> > > (as in fluctuation-dissipation theorem). If we use thermostats, the >> > > thermostats will correct the energy drop/raise caused by numerical >> error >> > > (which acts as a fluctuating source/sink that may not even follow the >> > > normal distribution), without causing additional artifacts. >> > > >> > > Regardless, thermostats causes artifacts, especially in dynamics and >> > rates. >> > > >> > > On Sun, Oct 12, 2014 at 2:07 PM, Michael Shirts >> > > wrote: >> > > >> > >> > The point was that if the energy leaves the system, then the system >> > >> is never in equilibrium. Not vice versa, please. >> > >> >> > >> This is incorrect logic. f there are errors in the integrator, then >> > >> F=gradient of the potential is not true. If that is not true, energy >> is >> > >> not >> > >> conserved, and energy can leave or enter the system. >> > >> >> > >> >> > >> On Sun, Oct 12, 2014 at 1:58 PM, Dr. Vitaly Chaban < >> vvcha...@gmail.com> >> > >> wrote: >> > >> >> > >> > The point was that if the energy leaves the system, then the >> system is >> > >> > never in equilibrium. Not vice versa, please. >> > >> > >> > >> > >> > >> > >> > >> > Dr. Vitaly V. Chaban >> > >> > >> > >> > Виталий Витальевич ЧАБАН >> > >> > >> > >> > >> > >> > On Sun, Oct 12, 2014 at 7:20 PM, Johnny Lu > > >> > >> wrote: >> > >> > > Why non-equilibrium can cause lost of total energy in NVE >> > simulation? >> > >> > > (baring the case that the non-equilibrium causes very large >> values >> > >> that >> > >> > > causes over flow / getting out of the stable range of algorithms >> of >> > >> > > gromacs). >> > >> > > >> > >> > > A closed system should have constant energy, regardless of >> whether >> > it >> > >> is >> > >> > at >> > >> > > equilibrium. >> > >> > > >> > >> > > I guess people use the word "converge" instead of equilibrium in >> > >> > molecular >> > >> > > dynamics simulation of protein, possibly because the simulation >> may >> > >> never >> > >> > > reach equilibrium with current computing power. >> > >> > > http://pubs.rsc.org/en/content/articlepdf/2012/cp/c2cp23961b >> > >> > > >> > >> > > I may try older version of gromacs and/or not using constraint, >> > after >> > >> > > checking the bug list and performance. I had never thought about >> > that >> > >> > route. >> > >> > > >> > >> > > >> > >> > > >> > >> > -- >> > >> > Gromacs Users mailing list >> > >> > >> > >> > * Please search the archive at >> > >> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List bef
Re: [gmx-users] Acetone parameters and transferability question
On 10/12/14 2:59 PM, Ioanna Styliari wrote: Thank you both very much for your very useful comments! Just to clarify, when you say "tweak the parameters", would just an investigation of the change of the charges be sufficient? There's no way to know that, but hopefully so. The charges from ATB would appear to me to be somewhat over-fitted, so adjusting them would be the first place I would look. Introducing new atom types means you have to make sure a lot more interactions are reasonable. Simple charge adjustments using existing atom types is straightforward, but it may be possible that you need to do more work. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] entangled polymer chain
hi, i wold know how in this file what does means the element in the III and IV colums? ffoplsaa.rtp: ; Polyethylene - this is an internal residue [ Eth ] [ atoms ] C1opls_136-0.1201 H11 opls_140 0.0601 H12 opls_140 0.0601 C2opls_136-0.1202 H21 opls_140 0.0602 H22 opls_140 0.0602 where i have to save this file? -- Marcello Cammarata, Ph.D. TEL 3208790796 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] entangled polymer chain
On 10/13/14 6:27 PM, unipa wrote: hi, i wold know how in this file what does means the element in the III and IV colums? ffoplsaa.rtp: ; Polyethylene - this is an internal residue [ Eth ] [ atoms ] C1opls_136-0.1201 H11 opls_140 0.0601 H12 opls_140 0.0601 C2opls_136-0.1202 H21 opls_140 0.0602 H22 opls_140 0.0602 where i have to save this file? It is an .rtp file; see manual section 5.6.1. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] asking for suggestings on conserved energy calcualtion in NVT when using V-rescale thermostat
Dear peers, I'd like to ask for your help on the calculation of conserved quantity H-tilde under V-rescale thermostate. As Mark suggested, the output of conserved En. in ener file is a overbid (http://permalink.gmane.org/gmane.science.biology.gromacs.user/63005). So, how can I get a real one? I have read the Bussi's original paper (JCP,2007), and I also tried to check out the calcuation of conserved En. in the soruce codes (e.g. coupling.c, md.c, Is it necessary? ), but I still don't know how to solve it. Any suggestions would be very precious for me. Thank you in advance. Wade -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Regarding umbrella samplling
Dear gromacs usres, I have run the umbrella sampling with the help of tutorial of justin. In my system rna is binding with gold nanoparticle. To find out the binding energy, i run the umbrella sampling using the space 0.1 nm and i got total 79 configurations, each configuration was run for 5 ns. Using g_wham, i got the profile.xvg, in that profile.xvg, all PMF values are zero. while running g_wham i am getting warings like below. WARNING, no data point in bin 163 (z=8.27767) ! You may not get a reasonable profile. Check your histograms! WARNING, no data point in bin 164 (z=8.31563) ! You may not get a reasonable profile. Check your histograms! WARNING, no data point in bin 165 (z=8.35358) ! You may not get a reasonable profile. Check your histograms! Warning, poor sampling bin 194 (z=9.45432). Check your histograms! Initialized rapid wham stuff (contrib tolerance 1.31579e-08) Evaluating only 2619 of 15200 expressions. 1) Maximum change 3.178184e+02 100) Maximum change 1.611126e+00 200) Maximum change 3.303540e+00 300) Maximum change 1.239682e+00 400) Maximum change 1.383353e+00 500) Maximum change 1.116406e+00 600) Maximum change 1.241516e+00 700) Maximum change 1.028108e+00 800) Maximum change 1.698508e+00 900) Maximum change 1.331078e+00 Switched to exact iteration in iteration 983 Converged in 984 iterations. Final maximum change 0 Please help me in this regard. Thanks sathish -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] same input tpr same results?
Hello: I've generate a .tpr file in my local machine and I am going to submit it to different cluster. I am just wondering, will the trajectory exactly the same? thank you very much albert -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
