Re: [gmx-users] Hamiltonian replica exchange
Hello Hind, There HREMD is available for Gromacs patched with PLUMED, and there is a tutorial you can go through: https://www.plumed.org/doc-v2.5/user-doc/html/hrex.html All the best, Qinghua On 1/18/20 8:12 PM, hind ahmed wrote: Dear, is there a tutorial to run Hamiltonian replica exchange in gromacs?? and could you please see if the mdp setting is right to run Hamiltonian replica exchange of lipid system using a coarse-grained method? integrator = sd tinit= 0.0 dt = 0.030 nsteps = 1500 nstxout = 5000 nstvout = 5000 nstfout = 5000 nstlog = 5000 nstenergy= 5000 nstxout-compressed = 5000 compressed-x-precision = 100 cutoff-scheme= Verlet nstlist = 20 ns_type = grid pbc = xyz verlet-buffer-tolerance = 0.005 epsilon_r= 15 coulombtype = reaction-field rcoulomb = 1.1 vdw_type = cutoff vdw-modifier = Potential-shift-verlet rvdw = 1.1 tc-grps = membrane solute tau_t= 1.0 1.0 ref_t= 323 323 ; Pressure coupling: Pcoupl = Parrinello-rahman Pcoupltype = isotropic tau_p= 12.0 compressibility = 4.5e-5 ref_p= 1.0 ; Free energy control stuff free_energy = no init_lambda_state= 0 delta_lambda = 0 calc_lambda_neighbors= 1; only immediate neighboring windows ; Vectors of lambda specified here ; Each combination is an index that is retrieved from init_lambda_state for each simulation ; init_lambda_state012345678910 11 coul-lambdas = 1.00 0.95 0.90 0.85 0.80 0.75 0.70 0.65 0.60 0.55 0.50 0.45 vdw-lambdas = 1.00 0.95 0.90 0.85 0.80 0.75 0.70 0.65 0.60 0.55 0.50 0.45 bonded-lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 restraint-lambdas= 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 ; Not doing simulated temperting here temperature_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 ; Options for the decoupling sc-alpha = 0.5 sc-coul = yes ; linear interpolation of Coulomb (none in this case) sc-power = 1 sc-sigma = 0.3 couple-moltype = CHOL ; name of moleculetype to decouple couple-lambda0 = vdw-q ; only van der Waals interactions couple-lambda1 = none ; turn off everything, in this case only vdW couple-intramol = no nstdhdl = 10 ; Do not generate velocities gen_vel = no ; options for bonds constraints = none ; Type of constraint algorithm constraint-algorithm = lincs ; Constrain the starting configuration ; since we are continuing from NPT continuation = yes ; Highest order in the expansion of the constraint coupling matrix refcoord_scaling = all Regards, Thanks -- 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] Hamiltonian replica exchange
Dear, is there a tutorial to run Hamiltonian replica exchange in gromacs?? and could you please see if the mdp setting is right to run Hamiltonian replica exchange of lipid system using a coarse-grained method? integrator = sd tinit= 0.0 dt = 0.030 nsteps = 1500 nstxout = 5000 nstvout = 5000 nstfout = 5000 nstlog = 5000 nstenergy= 5000 nstxout-compressed = 5000 compressed-x-precision = 100 cutoff-scheme= Verlet nstlist = 20 ns_type = grid pbc = xyz verlet-buffer-tolerance = 0.005 epsilon_r= 15 coulombtype = reaction-field rcoulomb = 1.1 vdw_type = cutoff vdw-modifier = Potential-shift-verlet rvdw = 1.1 tc-grps = membrane solute tau_t= 1.0 1.0 ref_t= 323 323 ; Pressure coupling: Pcoupl = Parrinello-rahman Pcoupltype = isotropic tau_p= 12.0 compressibility = 4.5e-5 ref_p= 1.0 ; Free energy control stuff free_energy = no init_lambda_state= 0 delta_lambda = 0 calc_lambda_neighbors= 1; only immediate neighboring windows ; Vectors of lambda specified here ; Each combination is an index that is retrieved from init_lambda_state for each simulation ; init_lambda_state012345678910 11 coul-lambdas = 1.00 0.95 0.90 0.85 0.80 0.75 0.70 0.65 0.60 0.55 0.50 0.45 vdw-lambdas = 1.00 0.95 0.90 0.85 0.80 0.75 0.70 0.65 0.60 0.55 0.50 0.45 bonded-lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 restraint-lambdas= 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 ; Not doing simulated temperting here temperature_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 ; Options for the decoupling sc-alpha = 0.5 sc-coul = yes ; linear interpolation of Coulomb (none in this case) sc-power = 1 sc-sigma = 0.3 couple-moltype = CHOL ; name of moleculetype to decouple couple-lambda0 = vdw-q ; only van der Waals interactions couple-lambda1 = none ; turn off everything, in this case only vdW couple-intramol = no nstdhdl = 10 ; Do not generate velocities gen_vel = no ; options for bonds constraints = none ; Type of constraint algorithm constraint-algorithm = lincs ; Constrain the starting configuration ; since we are continuing from NPT continuation = yes ; Highest order in the expansion of the constraint coupling matrix refcoord_scaling = all Regards, Thanks -- 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] Hamiltonian replica exchange in gromacs 4.6.7
Hi, You certainly want the code to take the path where lambda varies, but if you comment out the check for unequal lambda and avoid the check that T is unequal, things should work fine. Mark On Thu, Mar 8, 2018 at 2:59 AM Carlo Martinotti < carlo.martino...@postgrad.curtin.edu.au> wrote: > Hello everybody, > > So i am trying to set up a replica exchange with solute tempering > simulation for my membrane-drug systems. We modified the gromacs source > code in a way that allows the modification of the hamiltonian of singular > pairs of interactions (eg solute-water, solute-solute, ion-solute etc). > Until now I tested this part on single simulations and it's now working as > intended. Now though i have to switch on the replica exchange part and > allow them to exchange. > Right now i tried to set up a test system with 2 replicas at the same > temperatures, but with different scaling. > Again, remember this is an in house modification of the code, not the > classical REST methodology. > I launch the classical mdrun -multidir -replex and the system is > complaining that there is nothing to exchange cause the systems are the > same. I assume that this is because the temperature of two systems are > actually the same and he is using equation 3.141 from manual 4.6.7 part > 3.13. > > So here is my question: > > From my understanding of manual 4.6.7 part 3.13, to allow the exchange as > per equation 3.142 i MUST use the lambda routine. My idea is then to try to > trick the program inserting the same values of lambdas in both of the > replicas so to force gromacs tu use the equation 3.142 for the evaluation > of the probability of exchange. > I am pretty sure that the program is going to complain about that, but in > the case i can eliminate the check for identical lambdas in the source code. > > Do you think this would suffice? Or do you see things that i am missing > out ? > > Of course i know that without knowing what exact tweaks of the code we did > you can't answer accurately, but assume that when a single tempered > simulation is run the functions to compute the forces and the vdw terms are > changed in the beginning of the simulations and they stay changed for the > whole of the simulation, so that when gromacs will compute the cross terms > in ((U1(x2) − U1(x1)) + (U2(x1) − U2(x2)) it should be assumed to use the > right hamiltonian. > > Thanks in advance for the time and effort! > > -- > 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.
[gmx-users] Hamiltonian replica exchange in gromacs 4.6.7
Hello everybody, So i am trying to set up a replica exchange with solute tempering simulation for my membrane-drug systems. We modified the gromacs source code in a way that allows the modification of the hamiltonian of singular pairs of interactions (eg solute-water, solute-solute, ion-solute etc). Until now I tested this part on single simulations and it's now working as intended. Now though i have to switch on the replica exchange part and allow them to exchange. Right now i tried to set up a test system with 2 replicas at the same temperatures, but with different scaling. Again, remember this is an in house modification of the code, not the classical REST methodology. I launch the classical mdrun -multidir -replex and the system is complaining that there is nothing to exchange cause the systems are the same. I assume that this is because the temperature of two systems are actually the same and he is using equation 3.141 from manual 4.6.7 part 3.13. So here is my question: From my understanding of manual 4.6.7 part 3.13, to allow the exchange as per equation 3.142 i MUST use the lambda routine. My idea is then to try to trick the program inserting the same values of lambdas in both of the replicas so to force gromacs tu use the equation 3.142 for the evaluation of the probability of exchange. I am pretty sure that the program is going to complain about that, but in the case i can eliminate the check for identical lambdas in the source code. Do you think this would suffice? Or do you see things that i am missing out ? Of course i know that without knowing what exact tweaks of the code we did you can't answer accurately, but assume that when a single tempered simulation is run the functions to compute the forces and the vdw terms are changed in the beginning of the simulations and they stay changed for the whole of the simulation, so that when gromacs will compute the cross terms in ((U1(x2) − U1(x1)) + (U2(x1) − U2(x2)) it should be assumed to use the right hamiltonian. Thanks in advance for the time and effort! -- 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] Hamiltonian replica exchange with solute tempering in 5.x version (bug?)
Dear all, I would appreciate you to give me any comments or share your experience on the question below. I am trying to run Hamiltonian replica exchange with solute tempering (H-REST) in either 5.02 or 5.04 version to speed up the conformation sampling of my protein along with a caging small molecule. I made some changes in the force field parameters and used free energy function to effectively realize H-REST. However, after I prepared my equilibrated systems with different lambda values and tried to run H-REST, mdrun keeps saying that properties of every system are all the same. I also found a weird thing, not sure if it's a bug. All of the mdout.mdp files from different equilibrated systems have different lambda values at the beginning. However, after they are combined to run H-REST, the .log files turn out to have identical lambda values. The values are always that of the last replica (higher effective temperature). Here are an example of the mdp options I tried and the outcomes (.log file). Any other variants will still just make every replica the same as the last replica. mdp option for replica 1 Free-energy = yes Init-lambda-state = 0 fep-lambdas = 0 coul-lambdas = *0* couple-moltype = Other2 nstdhdl = 0 couple-lambda0 = vdw-q couple-lambda1 = vdw couple-intramol = yes mdp option for replica 8 Free-energy = yes Init-lambda-state = 0 fep-lambdas = 0 coul-lambdas = *0.577* couple-moltype = Other2 nstdhdl = 0 couple-lambda0 = vdw-q couple-lambda1 = vdw couple-intramol = yes .log file of replica 1 fep-lambdas =0 mass-lambdas =0 coul-lambdas =*0.577* vdw-lambdas =0 bonded-lambdas = restraint-lambdas =0 temperature-lambdas =0 .log file of replica 8 fep-lambdas =0 mass-lambdas =0 coul-lambdas =*0.577* vdw-lambdas =0 bonded-lambdas =0 restraint-lambdas =0 temperature-lambdas =0 I've also tried the following mdp option according to Michael's advice. https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2013-August/083430.html Free-energy = yes Init-lambda-state = 0 fep-lambdas = 0 0 0 0 0 0 0 0 coul-lambdas = 0 0.163 0.280 0.369 0.438 0.493 0.539 0.577 dhdl-derivatives = no couple-moltype = Other2 nstdhdl = 0 couple-lambda0 = vdw-q couple-lambda1 = vdw couple-intramol = yes but still not working. If this is really a bug not just a mistake of my wrong settings, maybe I should try PLUMED plug-in to invoke H-REST instead. Thanks for your reading Best regards, Tony -- 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] Hamiltonian replica exchange with umbrella sampling
Hi, I have come to understand that this might be doable with the newest gromacs versions 5.x (and without plumed). Can someone verify this? And if yes would he/she be so kind as to provide a sample .mdp file demonstrating how the pull code and the free energy code are communicating to succeed this? This restraint-lambdas option seems to be the best candidate for the solution and although I understand its purpose in the context of alchemical calculations, I can't figure out a way to use it in an umbrella sampling simulation. Best Maria -- 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] Hamiltonian Replica Exchange
Thank you all for your comment! The helix dimer is not very stable and I know that from extensive accelerated MD simulations I've done with AMBER using various boost values. Now I want to use a different force field available only in GROMACS, and though partial solute tempering HREX as the most suitable enhanced sampling technique considering the available computer resource I have. I know about the PLUMED implementation of partial tempering scheme. My question was if I can do the same with GROMACS because the speed with plumed is significantly impaired compared to serial execution of GROMACS: 3.10 ns/day / Replica with GROMACS 4.6.5 double precision + PLUMED 2.0.2 on a single node 5 ns/day with GROMACS 4.6.5 double precision on a single node (serial execution, only one replica) I don't know if it is the replica exchange scheme that affects the speed so much, or the communication with PLUMED. On another note, I would like to know you opinion about a couple of ideas I have: 1) In order to reduce the replicas needed to achieve 30-50% exchange rate for a given lambda range, I though to selectively heat only the main chain and CB carbons of the two disordered ends. Although I don't see anything wrong with this (except that the system may explode in low lambda replicas), I would be interested to know the opinion of more experienced people about possible caveats of the above mentioned rationale. 2) Do you reckon partial solute tempering HREX is suitable to monitor protein-ligand interactions? In my understanding, ligands will tend to stay more in touch with cold residues of the protein than with hot and hence the results may be misleading. Do you think I should also heat up the ligands to speed up their diffusion? thanks, Thomas -- == Thomas Evangelidis PhD student University of Athens Faculty of Pharmacy Department of Pharmaceutical Chemistry Panepistimioupoli-Zografou 157 71 Athens GREECE email: tev...@pharm.uoa.gr teva...@gmail.com website: https://sites.google.com/site/thomasevangelidishomepage/ -- 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] Hamiltonian Replica Exchange
On Fri, Jun 27, 2014 at 11:36 AM, Thomas Evangelidis teva...@gmail.com wrote: Thank you all for your comment! The helix dimer is not very stable and I know that from extensive accelerated MD simulations I've done with AMBER using various boost values. Now I want to use a different force field available only in GROMACS, and though partial solute tempering HREX as the most suitable enhanced sampling technique considering the available computer resource I have. I know about the PLUMED implementation of partial tempering scheme. My question was if I can do the same with GROMACS because the speed with plumed is significantly impaired compared to serial execution of GROMACS: 3.10 ns/day / Replica with GROMACS 4.6.5 double precision + PLUMED 2.0.2 on a single node 5 ns/day with GROMACS 4.6.5 double precision on a single node (serial execution, only one replica) Note that unfortunately your slowest replica will determine the overall speed of the run and if you have significant performance differences between replicas, you may end up wasting (5-3.1) ns/day. Also note that if you were comparing an Nx(1 thread/replica) run's performance with a single threaded run, the comparison is *not* valid! Most modern processors use frequency boosting and if you only use one (or a few) core(s) you'll get much higher clock frequency compared to what you get when all cores are used! Try to run vanilla GROMACS 4.6.5 with -multi too and you'll probably not get 5 ns/day anymore. Could you upload some log files to e.g. pastebin and share them here. Based on those we could tell where the overhead is - although you may want to verify what's the slowest replica's performance in a separate run because I think the multi-run's overhead can't be separated from the PLUMED overhead without code change. Cheers, -- Szilárd I don't know if it is the replica exchange scheme that affects the speed so much, or the communication with PLUMED. On another note, I would like to know you opinion about a couple of ideas I have: 1) In order to reduce the replicas needed to achieve 30-50% exchange rate for a given lambda range, I though to selectively heat only the main chain and CB carbons of the two disordered ends. Although I don't see anything wrong with this (except that the system may explode in low lambda replicas), I would be interested to know the opinion of more experienced people about possible caveats of the above mentioned rationale. 2) Do you reckon partial solute tempering HREX is suitable to monitor protein-ligand interactions? In my understanding, ligands will tend to stay more in touch with cold residues of the protein than with hot and hence the results may be misleading. Do you think I should also heat up the ligands to speed up their diffusion? thanks, Thomas -- == Thomas Evangelidis PhD student University of Athens Faculty of Pharmacy Department of Pharmaceutical Chemistry Panepistimioupoli-Zografou 157 71 Athens GREECE email: tev...@pharm.uoa.gr teva...@gmail.com website: https://sites.google.com/site/thomasevangelidishomepage/ -- 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] Hamiltonian Replica Exchange
PS: [Perhaps stating the obvious] Using an overly aggressive Hamiltonian scaling will only result in bad mixing at high temperatures and therefore low efficiency, hence wasted compute time, but it should not hurt your results. It is still quite useful to ensure that you're not sampling an entirely different system at small lambda factors. -- Szilárd On Wed, Jun 25, 2014 at 6:21 PM, Szilárd Páll pall.szil...@gmail.com wrote: Hi, Next time, you should perhaps use plz, ... (and other eye-catching formatting marks); a nice mix of font colors and typefaces could also help to highlight your questions. :D On Tue, Jun 24, 2014 at 10:32 PM, Thomas Evangelidis teva...@gmail.com wrote: Greetings, I want to use the HREX implementation of GROMACS to study the dynamics of a heterodimeric protein. The structure is a two helix bundle (two helical monomers that are wrapped around each other) with disordered ends. I am mainly interested in the dynamics of the disordered ends because I know from NMR that the rest remains structured. My question is, can I scale selectively the Hamiltonian of the disordered ends whilst leaving the Hamiltonian of the rest of the protein untouched in order to preserve the dimeric structure? I'm no expert in protein simulations, so take this with a grain of salt. ;) Unless your helix bundle is rather unstable, I think your proposal is fine. However, why not try it first? Generate the scaled topologies and run the one with the highest effective temperature separately to assess the stability of the bundles. Otherwise I 'll have to impose distance and secondary structure restraints which will slow down the computations and render the dynamics of the structured part unphysical. Is it possible to increase the force constant of the harmonic restraints as lambda decreases to attenuate the stiffness of the helices? Restraints are indeed sometimes required (and the above suggested experiment should tell whether that's the case, I think), but the lucky thing in the less than ideal topology hacking-based PLUMED approach is that you will actually by definition have N different inputs which can have differences not only in the scaled interactions, but e.g. in restraint strength. The other alternative will be to use much fewer replicas (up to lambda ~0.8 to be on the safe side) thus with slower sampling. If you want to be on the safe side and you observe is a sudden change in the stability of the helix bundle from a certain lambda, you can just stick to scaling factors lower than this. Assessing what maximum lambda is reasonable is something you should probably anyway do. Cheers, Sz. thanks, Thomas -- == Thomas Evangelidis PhD student University of Athens Faculty of Pharmacy Department of Pharmaceutical Chemistry Panepistimioupoli-Zografou 157 71 Athens GREECE email: tev...@pharm.uoa.gr teva...@gmail.com website: https://sites.google.com/site/thomasevangelidishomepage/ -- 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] Hamiltonian Replica Exchange
I would think of using Replica Exchange with Solute Tempering in this case. Look at the paper as to how one can implement this in Gromacs (doi: 10.1002/jcc.21703). Without having more details I would suggest to you to scale the Hamiltonian of each replica such that the Helix bundles are always correspond to the low temperature hamiltonian. The solute in your case would be the disordered ends that moves up the replica ladders during the exchange. The lambda dynamics module should be used and I would keep the topologies corresponding to the two ends such that at state B the hamiltonians of only the disordered ends are scaled (i.e. no scaling for the helical segments). On Tue, Jun 24, 2014 at 4:32 PM, Thomas Evangelidis teva...@gmail.com wrote: Greetings, I want to use the HREX implementation of GROMACS to study the dynamics of a heterodimeric protein. The structure is a two helix bundle (two helical monomers that are wrapped around each other) with disordered ends. I am mainly interested in the dynamics of the disordered ends because I know from NMR that the rest remains structured. My question is, can I scale selectively the Hamiltonian of the disordered ends whilst leaving the Hamiltonian of the rest of the protein untouched in order to preserve the dimeric structure? Otherwise I 'll have to impose distance and secondary structure restraints which will slow down the computations and render the dynamics of the structured part unphysical. Is it possible to increase the force constant of the harmonic restraints as lambda decreases to attenuate the stiffness of the helices? The other alternative will be to use much fewer replicas (up to lambda ~0.8 to be on the safe side) thus with slower sampling. thanks, Thomas -- == Thomas Evangelidis PhD student University of Athens Faculty of Pharmacy Department of Pharmaceutical Chemistry Panepistimioupoli-Zografou 157 71 Athens GREECE email: tev...@pharm.uoa.gr teva...@gmail.com website: https://sites.google.com/site/thomasevangelidishomepage/ -- 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] Hamiltonian Replica Exchange
Indeed. REST implemented in PLUMED seems a good bet. Mark On Jun 24, 2014 11:50 PM, HANNIBAL LECTER hanniballecte...@gmail.com wrote: I would think of using Replica Exchange with Solute Tempering in this case. Look at the paper as to how one can implement this in Gromacs (doi: 10.1002/jcc.21703). Without having more details I would suggest to you to scale the Hamiltonian of each replica such that the Helix bundles are always correspond to the low temperature hamiltonian. The solute in your case would be the disordered ends that moves up the replica ladders during the exchange. The lambda dynamics module should be used and I would keep the topologies corresponding to the two ends such that at state B the hamiltonians of only the disordered ends are scaled (i.e. no scaling for the helical segments). On Tue, Jun 24, 2014 at 4:32 PM, Thomas Evangelidis teva...@gmail.com wrote: Greetings, I want to use the HREX implementation of GROMACS to study the dynamics of a heterodimeric protein. The structure is a two helix bundle (two helical monomers that are wrapped around each other) with disordered ends. I am mainly interested in the dynamics of the disordered ends because I know from NMR that the rest remains structured. My question is, can I scale selectively the Hamiltonian of the disordered ends whilst leaving the Hamiltonian of the rest of the protein untouched in order to preserve the dimeric structure? Otherwise I 'll have to impose distance and secondary structure restraints which will slow down the computations and render the dynamics of the structured part unphysical. Is it possible to increase the force constant of the harmonic restraints as lambda decreases to attenuate the stiffness of the helices? The other alternative will be to use much fewer replicas (up to lambda ~0.8 to be on the safe side) thus with slower sampling. thanks, Thomas -- == Thomas Evangelidis PhD student University of Athens Faculty of Pharmacy Department of Pharmaceutical Chemistry Panepistimioupoli-Zografou 157 71 Athens GREECE email: tev...@pharm.uoa.gr teva...@gmail.com website: https://sites.google.com/site/thomasevangelidishomepage/ -- 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.
