Re: [gmx-users] REMD - replicas sampling in temperatures beyond the assigned range
Dear Justin, Thanks a lot for pointing out the issues. I now understand why there were such high oscillations. Could you please also tell me if there are any ideal values for pme_order and fourier spacing with respect to the cut offs' value of 1.4. Does the following Note imply I can raise the fourier grid spacing to 0.25? NOTE 2 [file sim-new.mdp]: The optimal PME mesh load for parallel simulations is below 0.5 and for highly parallel simulations between 0.25 and 0.33, for higher performance, increase the cut-off and the PME grid spacing Thank you again, Nisha On Thu, Jun 30, 2016 at 6:55 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 6/30/16 9:16 AM, NISHA Prakash wrote: > >> Dear Justin, >> >> Thank you for your reply. >> It is a protein carbohydrate system. Including the solvent, the number of >> atoms is 43499. >> I have minimized the system for 200 ps followed by NPT and NVT simulations >> for 200 ps respectively >> >> > Given that your temperature output started from 0 K, then you did not > continue from the equilibration properly by supplying the checkpoint file > to grompp -t. This is important to get right, otherwise you're basically > starting over from some random point (an equilibrated structure without any > velocities likely isn't a physically realistic state). > > Below is the .mdp file. >> >> >> ; VARIOUS PREPROCESSING OPTIONS >> title= REMD Simulation >> define = -DPOSRES >> >> >> ; RUN CONTROL PARAMETERS >> integrator = md-vv ; velocity verlet algorithm - >> tinit= 0 ; >> dt = 0.002; timestep in ps >> nsteps = 500; >> simulation-part = 1 ; Part index is updated automatically on >> checkpointing >> comm-mode= Linear ; mode for center of mass motion removal >> nstcomm = 100 ; number of steps for center of mass motion >> removal >> comm-grps= Protein_Carb Water_and_Ions ; group(s) for >> center of mass motion removal >> >> > In a solvated system, you should not be separating these groups. This > could explain the sudden jump in temperature - you could have things > clashing badly over the course of the simulation. > > > >> ; ENERGY MINIMIZATION OPTIONS >> emtol= 10 ; Force tolerance >> emstep = 0.01 ; initial step-size >> niter= 20 ; Max number of iterations in relax-shells >> fcstep = 0 ; Step size (ps^2) for minimization of >> flexible constraints >> nstcgsteep = 1000 ; Frequency of steepest descents steps >> when >> doing CG >> nbfgscorr= 10 >> >> >> ; OUTPUT CONTROL OPTIONS >> nstxout = 5 ; Writing full precision coordinates >> every >> ns >> nstvout = 5 ; Writing velocities every nanosecond >> nstfout = 0 ; Not writing forces >> nstlog = 5000 ; Writing to the log file every step 10ps >> nstcalcenergy= 100 >> nstenergy= 5000 ; Writing out energy information every >> step 10ps >> nstxtcout= 2500 ; Writing coordinates every 5 ps >> xtc-precision= 1000 >> xtc-grps = Protein_Carb Water_and_Ions ; subset of >> atoms for the .xtc file. >> energygrps = Protein_Carb Water_and_Ions ; Selection of >> energy groups >> >> >> ; NEIGHBORSEARCHING PARAMETERS >> nstlist = 10 ; nblist update frequency- >> ns-type = Grid ; ns algorithm (simple or grid) >> pbc = xyz ; Periodic boundary conditions: xyz, >> no, >> xy >> periodic-molecules = no >> rlist= 1.4 ; nblist cut-off >> rlistlong= -1 ; long-range cut-off for switched >> potentials >> >> >> ; OPTIONS FOR ELECTROSTATICS >> coulombtype = PME ; Method for doing electrostatics >> rcoulomb = 1.4 ; >> epsilon-r= 1 ; Relative dielectric constant for the >> medium >> pme_order= 10; >> >> >> ; OPTIONS FOR VDW >> vdw-type = Cut-off ; Method for doing Van der Waals >> rvdw-switch = 0 ; cut-off lengths >> rvdw = 1.4 ; >> DispCorr = EnerPres; Apply long range dispers
Re: [gmx-users] REMD - replicas sampling in temperatures beyond the assigned range
Dear Justin, Thank you for your reply. It is a protein carbohydrate system. Including the solvent, the number of atoms is 43499. I have minimized the system for 200 ps followed by NPT and NVT simulations for 200 ps respectively Below is the .mdp file. ; VARIOUS PREPROCESSING OPTIONS title= REMD Simulation define = -DPOSRES ; RUN CONTROL PARAMETERS integrator = md-vv ; velocity verlet algorithm - tinit= 0 ; dt = 0.002; timestep in ps nsteps = 500; simulation-part = 1 ; Part index is updated automatically on checkpointing comm-mode= Linear ; mode for center of mass motion removal nstcomm = 100 ; number of steps for center of mass motion removal comm-grps= Protein_Carb Water_and_Ions ; group(s) for center of mass motion removal ; ENERGY MINIMIZATION OPTIONS emtol= 10 ; Force tolerance emstep = 0.01 ; initial step-size niter= 20 ; Max number of iterations in relax-shells fcstep = 0 ; Step size (ps^2) for minimization of flexible constraints nstcgsteep = 1000 ; Frequency of steepest descents steps when doing CG nbfgscorr= 10 ; OUTPUT CONTROL OPTIONS nstxout = 5 ; Writing full precision coordinates every ns nstvout = 5 ; Writing velocities every nanosecond nstfout = 0 ; Not writing forces nstlog = 5000 ; Writing to the log file every step 10ps nstcalcenergy= 100 nstenergy= 5000 ; Writing out energy information every step 10ps nstxtcout= 2500 ; Writing coordinates every 5 ps xtc-precision= 1000 xtc-grps = Protein_Carb Water_and_Ions ; subset of atoms for the .xtc file. energygrps = Protein_Carb Water_and_Ions ; Selection of energy groups ; NEIGHBORSEARCHING PARAMETERS nstlist = 10 ; nblist update frequency- ns-type = Grid ; ns algorithm (simple or grid) pbc = xyz ; Periodic boundary conditions: xyz, no, xy periodic-molecules = no rlist= 1.4 ; nblist cut-off rlistlong= -1 ; long-range cut-off for switched potentials ; OPTIONS FOR ELECTROSTATICS coulombtype = PME ; Method for doing electrostatics rcoulomb = 1.4 ; epsilon-r= 1 ; Relative dielectric constant for the medium pme_order= 10; ; OPTIONS FOR VDW vdw-type = Cut-off ; Method for doing Van der Waals rvdw-switch = 0 ; cut-off lengths rvdw = 1.4 ; DispCorr = EnerPres; Apply long range dispersion corrections for Energy and Pressure table-extension = 1; Extension of the potential lookup tables beyond the cut-off fourierspacing = 0.08; Spacing for the PME/PPPM FFT grid ; GENERALIZED BORN ELECTROSTATICS gb-algorithm = Still; Algorithm for calculating Born radii nstgbradii = 1; Frequency of calculating the Born radii inside rlist rgbradii = 1; Cutoff for Born radii calculation gb-epsilon-solvent = 80; Dielectric coefficient of the implicit solvent gb-saltconc = 0; Salt concentration in M for Generalized Born models ; Scaling factors used in the OBC GB model. Default values are OBC(II) gb-obc-alpha = 1 gb-obc-beta = 0.8 gb-obc-gamma = 4.85 gb-dielectric-offset = 0.009 sa-algorithm = Ace-approximation sa-surface-tension = -1; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA - default -1 ; Temperature coupling tcoupl = nose-hoover nsttcouple = 10 ; nh-chain-length = 10 tc-grps = Protein_Carb Water_and_Ions ; Groups to couple separately tau-t= 1010; Time constant (ps)- ref-t = 270.0 270.0; reference temperature (K) ; pressure coupling pcoupl = no ;- ; GENERATE VELOCITIES FOR STARTUP RUN gen-vel = no gen-temp = 270.0 gen-seed = 173529 ; OPTIONS FOR BONDS continuation = yes ; constrain the start configuration constraints = all-bonds constraint-algorithm = lincs ; Type of constraint algorithm- lincs-order = 4 lincs-iter = 1 lincs-warnangle = 30 Thank you for your help. Nisha On Thu, Jun 30, 2016 at 6:21 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 6/30/16 8:46 AM, NISHA Prakash wrote: > >> Dear all, >> >> I have conducted a 10ns REMD simulation for a protein ligand complex
[gmx-users] REMD - replicas sampling in temperatures beyond the assigned range
Dear all, I have conducted a 10ns REMD simulation for a protein ligand complex with the temperature range - 270 to 350 K, however the temperature distribution plot of the replicas show that the sampling has occurred at higher temperatures as well that is beyond 350K - Below is an excerpt from the temperature xvg file @title "Gromacs Energies" @xaxis label "Time (ps)" @yaxis label "(K)" @TYPE xy @ view 0.15, 0.15, 0.75, 0.85 @ legend on @ legend box on @ legend loctype view @ legend 0.78, 0.8 @ legend length 2 @ s0 legend "Temperature" 0.000.00 10.00 350.997864 20.00 353.618927 30.00 350.068481 40.00 353.921753 50.00 359.485565 60.00 353.463654 70.00 352.015778 80.00 350.657898 90.00 351.927155 100.00 354.539429 110.00 354.287720 120.00 349.436096 130.00 352.960541 140.00 351.631317 150.00 354.217407 160.00 350.185852 170.00 350.294434 180.00 350.980194 190.00 350.914429 470.00 349.224060 480.00 350.819458 490.00 348.541748 500.00 350.393127 510.00 398.775208 520.00 444.802856 530.00 470.899323 540.00 466.652740 550.00 465.600677 560.00 469.22 570.00 470.548370 580.00 470.011566 590.00 470.643951 600.00 472.433197 610.00 470.451172 620.00 469.991699 630.00 469.073090 640.00 467.259521 650.00 464.561798 660.00 468.416901 670.00 468.754913 680.00 469.259613 690.00 467.641144 700.00 468.542328 Temperature coupling was done using Nose hoover algorithm. Does this imply the sampling is wrong or insufficent? Any help / suggestion is appreciated. Thanking you in anticipation. Nisha -- 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] System blowing up in Gromacsv5.0.5 but not in v4.5.4
Dear Justin, You are right and I totally agree with you. But, the point that I was trying to make was that "the same input coordinates and input .mdp files run in 4.5.4 and fail in 5.0.5". Also, if this situation persists, does that mean the results that have been obtained from the version 4.5.4 are not reliable? The second query was that - the topology and co-ordinates should be fine because I have obtained these files from the simulation of protein alone in version-5.0.5. Yet, I get LINCS warning for the protein atoms alone when I simulate it as a complex with the ligand. Kindly help me identify the problem. Thanking you, Nisha On Wed, Dec 16, 2015 at 7:05 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 12/16/15 12:08 AM, NISHA Prakash wrote: > >> Dear Justin, >> >> I am simulating a protein ligand complex. The protein co-ordinate file >> that >> I have taken is an output of the simulation of the protein alone in >> Gromacs-v5.0.5. The topology and the co-ordinates are fine. I am still >> facing this problem wherein I get the LINCS warning for only the protein >> atoms. The ligand also is fine. >> > > If the protein fails, you have a problem somewhere. That's either > topology (unlikely), coordinates (probable), or .mdp (most probable). You > said in your earlier message that energy minimization failed, which points > to coordinates being the problem. > > Like I mentioned before, I do not have this problem when I use the >> Gromacs-4.5.4 where I have used the same co-ordinate file with different >> ligands and same parameter file. >> >> > If you're comparing a protein-ligand complex in 5.0.5 against different > complexes in 4.5.4, that is a meaningless comparison. It's apples and > oranges. If the same input coordinates and input .mdp files run in 4.5.4 > and fail in 5.0.5, that might be something to look into. But the general > advice applies here - either way you're using outdated software, so if > something is failing, upgrade to the latest version and try again. > > -Justin > > > Kindly let me know how to resolve the issue. >> >> Thanking you in anticipation. >> >> Nisha >> >> >> >> >> On Wed, Dec 16, 2015 at 12:26 AM, Justin Lemkul <jalem...@vt.edu> wrote: >> >> >>> >>> On 12/15/15 8:42 AM, NISHA Prakash wrote: >>> >>> Hi all, >>>> >>>> I am trying to simulate a protein using similar parameters as in the >>>> tutorial - Protein ligand by Justin Lemkul. >>>> >>>> I am facing a problem wherein the protein simulation is exploding only >>>> in >>>> this version - Gromacs-v5.0.5 but not in the older version >>>> Gromacs-v4.5.4. >>>> >>>> The warning message is as follows >>>> >>>> --- >>>> There were 4 inconsistent shifts. Check your topology >>>> >>>> Steepest Descents: >>>> Tolerance (Fmax) = 1.0e+03 >>>> Number of steps=5 >>>> >>>> WARNING: Listed nonbonded interaction between particles 1312 and 1315 >>>> at distance 4.728 which is larger than the table limit 2.000 nm. >>>> >>>> This is likely either a 1,4 interaction, or a listed interaction inside >>>> a smaller molecule you are decoupling during a free energy calculation. >>>> Since interactions at distances beyond the table cannot be computed, >>>> they are skipped until they are inside the table limit again. You will >>>> only see this message once, even if it occurs for several interactions. >>>> >>>> IMPORTANT: This should not happen in a stable simulation, so there is >>>> probably something wrong with your system. Only change the >>>> table-extension >>>> distance in the mdp file if you are really sure that is the reason. >>>> >>>> ATOM 1312 O TYR A 207 >>>> ATOM 1315 CD1 TYR A 207 >>>> - >>>> >>>> >>>> >>>> --- >>>> em_real.mdp file >>>> >>>> ; LINES STARTING WITH ';' ARE COMMENTS >>>> title = Minimization ; Title of run >>>> >>>> ; Parameters describing what to do, when to stop and what to save >>>> integrator = steep ; Algorithm (steep = steepest descent
Re: [gmx-users] System blowing up in Gromacsv5.0.5 but not in v4.5.4
Dear Justin, I am simulating a protein ligand complex. The protein co-ordinate file that I have taken is an output of the simulation of the protein alone in Gromacs-v5.0.5. The topology and the co-ordinates are fine. I am still facing this problem wherein I get the LINCS warning for only the protein atoms. The ligand also is fine. Like I mentioned before, I do not have this problem when I use the Gromacs-4.5.4 where I have used the same co-ordinate file with different ligands and same parameter file. Kindly let me know how to resolve the issue. Thanking you in anticipation. Nisha On Wed, Dec 16, 2015 at 12:26 AM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 12/15/15 8:42 AM, NISHA Prakash wrote: > >> Hi all, >> >> I am trying to simulate a protein using similar parameters as in the >> tutorial - Protein ligand by Justin Lemkul. >> >> I am facing a problem wherein the protein simulation is exploding only in >> this version - Gromacs-v5.0.5 but not in the older version Gromacs-v4.5.4. >> >> The warning message is as follows >> >> --- >> There were 4 inconsistent shifts. Check your topology >> >> Steepest Descents: >> Tolerance (Fmax) = 1.0e+03 >> Number of steps=5 >> >> WARNING: Listed nonbonded interaction between particles 1312 and 1315 >> at distance 4.728 which is larger than the table limit 2.000 nm. >> >> This is likely either a 1,4 interaction, or a listed interaction inside >> a smaller molecule you are decoupling during a free energy calculation. >> Since interactions at distances beyond the table cannot be computed, >> they are skipped until they are inside the table limit again. You will >> only see this message once, even if it occurs for several interactions. >> >> IMPORTANT: This should not happen in a stable simulation, so there is >> probably something wrong with your system. Only change the table-extension >> distance in the mdp file if you are really sure that is the reason. >> >> ATOM 1312 O TYR A 207 >> ATOM 1315 CD1 TYR A 207 >> - >> >> >> >> --- >> em_real.mdp file >> >> ; LINES STARTING WITH ';' ARE COMMENTS >> title = Minimization ; Title of run >> >> ; Parameters describing what to do, when to stop and what to save >> integrator = steep ; Algorithm (steep = steepest descent minimization) >> emtol = 1000.0 ; Stop minimization when the maximum force < 10.0 kJ/mol >> emstep = 0.01 ; Energy step size >> nsteps = 5 ; Maximum number of (minimization) steps to perform >> energygrps = Protein ; Which energy group(s) to write to disk >> >> ; Parameters describing how to find the neighbors of each atom and how to >> calculate the interactions >> nstlist= 1; Frequency to update the neighbor list and long range >> forces >> cutoff-scheme = Verlet >> ns_type= grid ; Method to determine neighbor list (simple, grid) >> rlist= 1.0 ; Cut-off for making neighbor list (short range forces) >> coulombtype= PME ; Treatment of long range electrostatic interactions >> rcoulomb= 1.0 ; long range electrostatic cut-off >> rvdw= 1.0 ; long range Van der Waals cut-off >> pbc= xyz ; Periodic Boundary Conditions >> >> >> >> >> The initial minimization step itself fails. >> > > If minimization fails, you have a problem with the topology or > coordinates. Perhaps you got a bit lucky with some quirk of an algorithmic > difference in the old version that is failing here. > > -Justin > > I have tried to simulate a minimized structure as well, I still encounter >> the same problem. >> >> I would appreciate any help in this regard. >> I would also like to know if this means, that the results from the older >> version of gromacs reliable? >> >> Thanking you in anticipation >> >> Nisha >> >> > -- > == > > 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
[gmx-users] System blowing up in Gromacsv5.0.5 but not in v4.5.4
Hi all, I am trying to simulate a protein using similar parameters as in the tutorial - Protein ligand by Justin Lemkul. I am facing a problem wherein the protein simulation is exploding only in this version - Gromacs-v5.0.5 but not in the older version Gromacs-v4.5.4. The warning message is as follows --- There were 4 inconsistent shifts. Check your topology Steepest Descents: Tolerance (Fmax) = 1.0e+03 Number of steps=5 WARNING: Listed nonbonded interaction between particles 1312 and 1315 at distance 4.728 which is larger than the table limit 2.000 nm. This is likely either a 1,4 interaction, or a listed interaction inside a smaller molecule you are decoupling during a free energy calculation. Since interactions at distances beyond the table cannot be computed, they are skipped until they are inside the table limit again. You will only see this message once, even if it occurs for several interactions. IMPORTANT: This should not happen in a stable simulation, so there is probably something wrong with your system. Only change the table-extension distance in the mdp file if you are really sure that is the reason. ATOM 1312 O TYR A 207 ATOM 1315 CD1 TYR A 207 - --- em_real.mdp file ; LINES STARTING WITH ';' ARE COMMENTS title = Minimization ; Title of run ; Parameters describing what to do, when to stop and what to save integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 1000.0 ; Stop minimization when the maximum force < 10.0 kJ/mol emstep = 0.01 ; Energy step size nsteps = 5 ; Maximum number of (minimization) steps to perform energygrps = Protein ; Which energy group(s) to write to disk ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist= 1; Frequency to update the neighbor list and long range forces cutoff-scheme = Verlet ns_type= grid ; Method to determine neighbor list (simple, grid) rlist= 1.0 ; Cut-off for making neighbor list (short range forces) coulombtype= PME ; Treatment of long range electrostatic interactions rcoulomb= 1.0 ; long range electrostatic cut-off rvdw= 1.0 ; long range Van der Waals cut-off pbc= xyz ; Periodic Boundary Conditions The initial minimization step itself fails. I have tried to simulate a minimized structure as well, I still encounter the same problem. I would appreciate any help in this regard. I would also like to know if this means, that the results from the older version of gromacs reliable? Thanking you in anticipation Nisha -- 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] REMD system blowing up
Hi all, I would like to know if there is a way to figure out which of the replica is exploding during REMD simulation? I am running REMD for 54 replicas and the system is exploding with just one step14495b.pdb and step14495c.pdb files. Does this mean there is just one replica that is exploding? Does this also have to do with the temperature? The equilibration was carried out for 600 ps and the individual replicas have no issues. Awaiting response. Thanks! Nisha -- 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] Fwd: Is_trjcat_suitable_for_concatenating_REMD_trajectorie
Hi, Can somebody please help with WHAM reweighting scheme for REMD analysis. The command gmx wham works for Umbrella sampling simulation but I couldnt find a way out for T-REMD. There are similar questions which have been posted here but unfortunately, I haven't found answers for the same. WHAM for REMD has been well documented for AMBER but I couldnt find any help for Gromacs. I am a novice in the field and help is appreciated. Thanks! Nisha -- 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] Fwd: Is_trjcat_suitable_for_concatenating_REMD_trajectorie
Hi Mark, Thanks for your quick response. Can you please suggest a way out? As you pointed out previously, I have 18 ensembles and I would like to study the conformational changes, the interactions between the protein and the ligand and finally, I would like to extract the stable conformation from the simulation data. How do I go about analysing the REMD results. Your tutorial was indeed very helpful but apart from that, I couldn't find much information in that area. Thanks again, Nisha On Fri, Apr 3, 2015 at 2:38 PM, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, There's nothing in GROMACS that specifically supports reweighting replica-exchange simulations. Mark On 03/04/2015 10:03 am, NISHA Prakash nishnith20...@gmail.com wrote: Hi, Can somebody please help with WHAM reweighting scheme for REMD analysis. The command gmx wham works for Umbrella sampling simulation but I couldnt find a way out for T-REMD. There are similar questions which have been posted here but unfortunately, I haven't found answers for the same. WHAM for REMD has been well documented for AMBER but I couldnt find any help for Gromacs. I am a novice in the field and help is appreciated. Thanks! Nisha -- 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] Fwd: Is_trjcat_suitable_for_concatenating_REMD_trajectorie
Hi Mark, All I want to know is the first step that I have to take in analyzing the trajectories. By way of mentioning what I want to do was to essentially list out my aim only to make my question clear. With REMD results, I want to know whether analyzing individual ensemble is the way to go or look at the ensembles together, this is because I would like to bring out a comparison between the simulations with protein bound to three different ligands. I hope I have made myself clear. Thanks again, Nisha On Fri, Apr 3, 2015 at 9:33 PM, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, You seem to be essentially asking for your experiment to be designed for you, after an arbitrary simulation is complete. You should think about what and how to observe before you simulate, e.g. from what others have done for similar systems. Consideration of reweighting is secondary. Generally, the only difference with REMD simulations is that you cannot assume that the set of frames from an ensemble are from a contiguous trajectory. Mark On 03/04/2015 11:21 am, NISHA Prakash nishnith20...@gmail.com wrote: Hi Mark, Thanks for your quick response. Can you please suggest a way out? As you pointed out previously, I have 18 ensembles and I would like to study the conformational changes, the interactions between the protein and the ligand and finally, I would like to extract the stable conformation from the simulation data. How do I go about analysing the REMD results. Your tutorial was indeed very helpful but apart from that, I couldn't find much information in that area. Thanks again, Nisha On Fri, Apr 3, 2015 at 2:38 PM, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, There's nothing in GROMACS that specifically supports reweighting replica-exchange simulations. Mark On 03/04/2015 10:03 am, NISHA Prakash nishnith20...@gmail.com wrote: Hi, Can somebody please help with WHAM reweighting scheme for REMD analysis. The command gmx wham works for Umbrella sampling simulation but I couldnt find a way out for T-REMD. There are similar questions which have been posted here but unfortunately, I haven't found answers for the same. WHAM for REMD has been well documented for AMBER but I couldnt find any help for Gromacs. I am a novice in the field and help is appreciated. Thanks! Nisha -- 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. -- 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] Fwd: Is_trjcat_suitable_for_concatenating_REMD_trajectorie
Dear all, I have simulated the protein ligand complex at 18 different temperatures. I was wondering if it was right to concatenate the trajectories of 18 replicas because they are at different temperatures, with different initial structures but have the same start time. Use of -demux flag is resulting in independent .xtc files instead of one continuous trajectory file. Use of -cat is giving a WARNING: same Start time as previous. How do I get a single continuous trajectory for analysis or should the trajectories from each of the replica be analysed separately? I am new to REMD so any help with respect to analysis in the form of tutorial will be highly appreciated. Awaiting response. 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.
