Re: [gmx-users] Using thermostats to create temperature gradient in system
Hi Agnivo, Temperature gradient means non-equilibrium MD (NEMD) See notes from Prof. Martini: https://nanohub.org/resources/7582/download/Martini_L10_NonequilibruimMD.pdf What observable would you like to measure? Lets say you want to measure observable A. One procedure I can think of: 1. You can run all system at T=300K with NVT. After equilibrium, continue running all system at T=400K with freezing solvent group. See, to how to freeze a group, http://manual.gromacs.org/online/mdp_opt.html#neq To get a good statistic, you need to repeat this procedure K times as solvent thermal wall configuration would be different at each simulation. 100ps? Where did you get that? You need to see how observable A behaves to see if 100ps is enough, A time average. And see how A behaves in K different cases. 2. Similar to previous procedure but this time after freezing solvent group, run system in NVE. Again, you need to repeat this many times to get a good statistic. Similarly monitor observable A to see if 500ps is enough. However, I suggest you to talk to someone having NEMD experience as this procedure is just a heuristic approach. -m -- 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] Using thermostats to create temperature gradient in system
Hi Agnivo; Yes, the idea of freezing the solvent or the protein in many times is to sample the non-equilibrium thermal process. It will remain in the target temperature on average, over many fixed configurations obtained by different NVT runs (equilibrium runs). But you may need to run this many K times to get a good statistic as I said. Concerning NVE, yes, do the same fixing approach with the protein. But as I mentioned earlier, this is quite heuristic approach, I suggest you to talk with any faculty member having background in non-equilibrium processes if this approach mimics what you need. Best, -m -- 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] Using thermostats to create temperature gradient in system
Hello Users, This is in relation to my previous posts. I am looking to replicate the figure below : tempgradient.png https://docs.google.com/file/d/0B-U8uULVZjfRQWlHeHVJdDJjcms/edit?usp=drive_web Basically I am following this paper for my work : Lervik_ProtWatInterHT_2009.pdf https://docs.google.com/file/d/0B-U8uULVZjfRU2haRkNHd2wwNTA/edit?usp=drive_web Look at figure 6 of the paper. My system has water at 300 K and protein at 400 K. The authors of the paper describe that they removed the thermostat from the protein and let it relax keeping the solvent (water) at 300 K. But if I remove thermostat , I get GROMACS error and using freeze groups I am not getting any temperatures as the molecules are not moving. I can not understand how to model this system. Any suggestions will be helpful. I am doing a literature search but till now it is not fruitful. Best, Thanks Regards Agnivo Gosai Grad Student, Iowa State University. -- 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] Using thermostats to create temperature gradient in system
Hello all, Thanks to Dr. Lemkul for asking. This is what I did to reach my present state : (a) Prepared the topology of the system using GROMOS96 43a2 ff and energy minimized the system after solvation using steepest descent algorithm. (b) Did a position restrained ( protein ) 5 ns Fatal error: 2936 atoms are not part of any of the T-Coupling groups For more information and tips for troubleshooting, please check the GROMACS Thanks Regards Agnivo Gosai Grad Student, Iowa State University. -- 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] Using thermostats to create temperature gradient in system
Hello all, Thanks to Dr. Lemkul for asking. This is what I did to reach my present state : (a) Prepared the topology of the system using GROMOS96 43a2 ff and energy minimized the system after solvation using steepest descent algorithm. (b) Did a position restrained ( protein restrained ) 5 ns NVT equilibration using V-rescale thermostat at target temp. of 300 K. (c) Then I kept the solvent at 300 K in a NVT ensemble and heated the protein only by simulated annealing over 500 ps , to 400K. I checked the individual temperatures and found that it was achieved. (d) Then as mentioned in the paper if I remove the thermostat on the protein then grompp gives the following error :- Fatal error: 2936 atoms are not part of any of the T-Coupling groups For more information and tips for troubleshooting, please check the GROMACS I want to let my protein loose heat and thus go down a temp. gradient while the solvent i.e. water stays at 300 K. However , I am unable to do this. If I do not specify any thermostat in a NVT ensemble it becomes NVE and I only get a single temperature profile. Any hints as to how I can achieve my objective ? Sorry for the previous incomplete post. Thanks Regards Agnivo Gosai Grad Student, Iowa State University. -- 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] Using thermostats to create temperature gradient in system
On 4/26/15 7:07 PM, Agnivo Gosai wrote: Hello Users, This is in relation to my previous posts. I am looking to replicate the figure below : tempgradient.png https://docs.google.com/file/d/0B-U8uULVZjfRQWlHeHVJdDJjcms/edit?usp=drive_web Basically I am following this paper for my work : Lervik_ProtWatInterHT_2009.pdf https://docs.google.com/file/d/0B-U8uULVZjfRU2haRkNHd2wwNTA/edit?usp=drive_web Look at figure 6 of the paper. My system has water at 300 K and protein at 400 K. The authors of the paper describe that they removed the thermostat from the protein and let it relax keeping the solvent (water) at 300 K. But if I remove thermostat , I get GROMACS error and using freeze groups I am not getting any temperatures as the molecules are not moving. You'll have to show us what you're doing to get GROMACS error (what error? what were your input settings? Don't make us guess!) Freezing groups means they have no temperature and they don't move. This certainly isn't what you want. I can not understand how to model this system. Any suggestions will be helpful. I am doing a literature search but till now it is not fruitful. Setting tau_t = -1 for the protein tc-grp will remove the thermostat; e.g. not couple it. This sounds like what you want. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 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] Using thermostats to create temperature gradient in system
On 4/26/15 8:14 PM, Agnivo Gosai wrote: Hello all, Thanks to Dr. Lemkul for asking. This is what I did to reach my present state : (a) Prepared the topology of the system using GROMOS96 43a2 ff and energy minimized the system after solvation using steepest descent algorithm. (b) Did a position restrained ( protein ) 5 ns Fatal error: 2936 atoms are not part of any of the T-Coupling groups For more information and tips for troubleshooting, please check the GROMACS This means your tc-grps are set up incorrectly, but again you haven't provided your actual settings (copy and paste your .mdp when reporting problems - always). -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 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] Using thermostats to create temperature gradient in system
Hello, I am copy pasting my mdp file for the last step of my procedure : Here I am not using any freeze group. ; Run parameters integrator = md; leap-frog integrator nsteps = 5; 100 ps dt = 0.002 ; 2 fs energygrps = Protein Non-Protein ; Output control nstxout = 10 nstvout = 10 nstlog = 10 nstenergy = 10 nstxtcout = 50 ; Bond parameters continuation= yes ; after trial 400 K constraint_algorithm = lincs; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching ns_type = grid ; search neighboring grid cells nstlist = 5 ; 10 fs rlist = 1.4 ; short-range neighborlist cutoff (in nm) rcoulomb= 1.4 ; short-range electrostatic cutoff (in nm) rvdw= 1.4 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 ewald_rtol = 1e-5 ; relative strength of Ewald - shifted direct potential optimize_fft= yes ; saves computation time ; Temperature coupling is on tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = Non-Protein tau_t = 0.1 ; time constant, in ps ref_t = 300 ; reference temperature,in K ; Pressure coupling is off pcoupl = no ; no pressure coupling in NVT ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr= EnerPres ; account for cut-off vdW scheme ; COM motion removal ; These options remove COM motion of the system nstcomm = 100 comm-mode = Linear comm-grps = System Plz have a look. Thanks Regards Agnivo Gosai Grad Student, Iowa State University. -- 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] Using thermostats to create temperature gradient in system
Dr. Lemkul Thanks for such an easy fix to my problem. I guess I have been doing all sort of weird stuff since last night instead of thinking logically and reading the relevant portion of the manual. Thanks Regards Agnivo Gosai Grad Student, Iowa State University. -- 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] Using thermostats to create temperature gradient in system
Hello users, Thanks a lot Suzen for an insightful suggestion. My protein and solvent have been equilibrated at 300 K in an NVT ensemble. I raised the temperature of protein gradually by using simulated annealing to 400 K and the solvent has been kept at 300 K. Now I wish to get a temperature gradient such that the temperature of the protein comes down by exchanging heat with the solvent to 300 K. So as per your suggestion , do I need to freeze the solvent group so that its position will not be updated and hence it will have the same temperature ?? For the protein if I do not use a thermostat , GROMACS will give error message. So how do I fix this problem ? Or, should I freeze the protein instead and use a thermostat on the solvent ? I am trying both of these as I write this mail. Thanks Regards Agnivo Gosai Grad Student, Iowa State University. -- 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] Using thermostats to create temperature gradient in system
Hello Users I have equilibrated a protein solvent system using NVT ensemble and V - rescale thermostat. Target temperature was 300 K. Now I want to establish a temperature gradient in my system as follows : 1. Use Two Berendsen thermostats separately for Protein and Non Protein grps. Protein grp , T = 400 K Non protein grp, T = 300 K. Run in NVT for 100 ps. 2. Then remove thermostat from Protein grp. But keep thermostat for Non Protein grp. Run in NVT for 500 ps. I hope that the protein will come down or relax to 300 K. Is the above scheme feasible ? I have not yet tried. I use COM motion removal for the whole system. Thanks Regards Agnivo Gosai Grad Student, Iowa State University. -- 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.
