Re: [gmx-users] Replica exchange MD analysis
Thank you Justin, with your valuable input I got the solution. regards RajP On Mon, Mar 25, 2019 at 11:44 PM Justin Lemkul wrote: > > > > On 3/25/19 2:22 PM, Rituraj Purohit wrote: > > Thank you Mark for the reply. In my REMD results I would like to > > observe the structure transition with temperature given variation (I > > think it is most common observation). My query here is the output of > > REMD, It does not give .xtc file but only .edr, .log and .gro > > even-thou I indicated -x .xtc during job submission. Is it possible to > > perform analysis with .edr, .log & .gro files and without the > > Trajectory file? If yes, Please let me know how to do different > > analysis such as RMSD, RMSF, Rg etc.. > > All of those depend on coordinates over time, i.e. the trajectory. Your > existing files cannot be used for such analysis. You will only get an > .xtc file if you specify a non-zero value of nstxout-compressed in the > .mdp file. > > -Justin > > > regards > > RajP > > > > On Mon, Mar 25, 2019 at 6:43 PM Mark Abraham > > wrote: > >> Hi, > >> > >> This is the same as for any other scientific experiment. You need to have > >> thought about what you hope to learn and what you need to record in order > >> to analyse the results. REMD is essentially no different here. > >> > >> Mark > >> > >> On Sun., 24 Mar. 2019, 10:51 Rituraj Purohit, > >> wrote: > >> > >>> Dear Friends, > >>> I performed REMD by following tutorial provided by Mark Abraham, But I > >>> am not able to get the analysis part. Is a step-wise tutorial > >>> available ? I would be thankful to you if anyone of you could help me > >>> to perform analysis of REMD output. Thanking you > >>> Regards > >>> RajP > >>> -- > >>> 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. > > -- > == > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > == > > -- > 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] Replica exchange MD analysis
On 3/25/19 2:22 PM, Rituraj Purohit wrote: Thank you Mark for the reply. In my REMD results I would like to observe the structure transition with temperature given variation (I think it is most common observation). My query here is the output of REMD, It does not give .xtc file but only .edr, .log and .gro even-thou I indicated -x .xtc during job submission. Is it possible to perform analysis with .edr, .log & .gro files and without the Trajectory file? If yes, Please let me know how to do different analysis such as RMSD, RMSF, Rg etc.. All of those depend on coordinates over time, i.e. the trajectory. Your existing files cannot be used for such analysis. You will only get an .xtc file if you specify a non-zero value of nstxout-compressed in the .mdp file. -Justin regards RajP On Mon, Mar 25, 2019 at 6:43 PM Mark Abraham wrote: Hi, This is the same as for any other scientific experiment. You need to have thought about what you hope to learn and what you need to record in order to analyse the results. REMD is essentially no different here. Mark On Sun., 24 Mar. 2019, 10:51 Rituraj Purohit, wrote: Dear Friends, I performed REMD by following tutorial provided by Mark Abraham, But I am not able to get the analysis part. Is a step-wise tutorial available ? I would be thankful to you if anyone of you could help me to perform analysis of REMD output. Thanking you Regards RajP -- 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. -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- 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] Replica exchange MD analysis
Thank you Mark for the reply. In my REMD results I would like to observe the structure transition with temperature given variation (I think it is most common observation). My query here is the output of REMD, It does not give .xtc file but only .edr, .log and .gro even-thou I indicated -x .xtc during job submission. Is it possible to perform analysis with .edr, .log & .gro files and without the Trajectory file? If yes, Please let me know how to do different analysis such as RMSD, RMSF, Rg etc.. regards RajP On Mon, Mar 25, 2019 at 6:43 PM Mark Abraham wrote: > > Hi, > > This is the same as for any other scientific experiment. You need to have > thought about what you hope to learn and what you need to record in order > to analyse the results. REMD is essentially no different here. > > Mark > > On Sun., 24 Mar. 2019, 10:51 Rituraj Purohit, > wrote: > > > Dear Friends, > > I performed REMD by following tutorial provided by Mark Abraham, But I > > am not able to get the analysis part. Is a step-wise tutorial > > available ? I would be thankful to you if anyone of you could help me > > to perform analysis of REMD output. Thanking you > > Regards > > RajP > > -- > > 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] Replica exchange MD analysis
Hi, This is the same as for any other scientific experiment. You need to have thought about what you hope to learn and what you need to record in order to analyse the results. REMD is essentially no different here. Mark On Sun., 24 Mar. 2019, 10:51 Rituraj Purohit, wrote: > Dear Friends, > I performed REMD by following tutorial provided by Mark Abraham, But I > am not able to get the analysis part. Is a step-wise tutorial > available ? I would be thankful to you if anyone of you could help me > to perform analysis of REMD output. Thanking you > Regards > RajP > -- > 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] Replica exchange MD analysis
RajP, For future questions, if you don't get a response, then change the question, add further details etc. Repeating the same question several times doesn't improve your chances of getting a response. Your question is very broad, general and lacks specifics, hence why no one has responded. Show that you've done some work, tried things, used existing resources, etc. No one is here to do your research for you. Questions to ask yourself : Why are you performing REMD? What property or properties will provide insight into that? What analysis can you perform to gain insight into the behaviour of those properties? What is published in the same/similar area? What analysis, scripts and software have you tried? What exactly are you having difficulty with? "I am not able to get the analysis part" doesn't really tell us anything. On Sun, 24 Mar. 2019, 8:51 pm Rituraj Purohit, wrote: > Dear Friends, > I performed REMD by following tutorial provided by Mark Abraham, But I > am not able to get the analysis part. Is a step-wise tutorial > available ? I would be thankful to you if anyone of you could help me > to perform analysis of REMD output. Thanking you > Regards > RajP > -- > 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] Replica exchange MD analysis
Dear Friends, I performed REMD by following tutorial provided by Mark Abraham, But I am not able to get the analysis part. Is a step-wise tutorial available ? I would be thankful to you if anyone of you could help me to perform analysis of REMD output. Thanking you Regards RajP -- 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] Replica exchange MD analysis
Dear Friends, I performed REMD by following tutorial provided by Mark Abraham, But I am not able to get the analysis part. Is a step-wise tutorial available ? I would be thankful to you if anyone of you could help me to perform analysis of REMD output. Thanking you Regards RajP -- 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] Replica exchange MD analysis
Dear Friends, I performed REMD by following tutorial provided by Mark Abraham, But I am not able to get the analysis part. Is a step-wise tutorial available ? I would be thankful to you if anyone of you could help me to perform analysis of REMD output. Thanking you Regards RajP -- 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] Replica Exchange MD
> > > QMMM = no > > QMMM-grps= > > QMmethod = > > QMMMscheme = normal > > QMbasis = > > QMcharge = > > QMmult = > > SH = > > CASorbitals = > > CASelectrons = > > SAon = > > SAoff= > > SAsteps = > > MMChargeScaleFactor = 1 > > bOPT = > > bTS = > > annealing= > > annealing-npoints= > > annealing-time = > > annealing-temp = > > gen-vel = yes > > gen-temp = 280.00 > > gen-seed = 173529 > > constraints = all-bonds > > constraint-algorithm = Lincs > > continuation = no > > Shake-SOR= no > > shake-tol= 0.0001 > > lincs-order = 4 > > lincs-iter = 1 > > lincs-warnangle = 30 > > morse= no > > energygrp-excl = > > nwall= 0 > > wall-type= 9-3 > > wall-r-linpot= -1 > > wall-atomtype= > > wall-density = > > wall-ewald-zfac = 3 > > pull = no > > ;rotation = no > > disre= No > > disre-weighting = Conservative > > disre-mixed = no > > disre-fc = 1000 > > disre-tau= 0 > > nstdisreout = 100 > > orire= no > > orire-fc = 0 > > orire-tau= 0 > > orire-fitgrp = > > nstorireout = 100 > > free-energy = no > > couple-moltype = > > couple-lambda0 = vdw-q > > couple-lambda1 = vdw-q > > couple-intramol = no > > init-lambda = -1 > > ;init-lambda-state= -1 > > delta-lambda = 0 > > nstdhdl = 50 > > fep-lambdas = > > mass-lambdas = > > coul-lambdas = > > vdw-lambdas = > > bonded-lambdas = > > restraint-lambdas= > > temperature-lambdas = > > ;calc-lambda-neighbors= 1 > > init-lambda-weights = > > ;dhdl-print-energy= no > > sc-alpha = 0 > > sc-power = 1 > > ;sc-r-power = 6 > > sc-sigma = 0.3 > > ;sc-coul = no > > separate-dhdl-file = yes > > dhdl-derivatives = yes > > dh_hist_size = 0 > > dh_hist_spacing = 0.1 > > acc-grps = > > accelerate = > > freezegrps = > > freezedim= > > cos-acceleration = 0 > > deform = > > ;simulated-tempering = no > > ;simulated-tempering-scaling = geometric > > ;sim-temp-low = 300 > > ;sim-temp-high= 300 > > E-x = > > E-xt = > > E-y = > > E-yt = > > E-z = > > E-zt = > > ;adress = no > > user1-grps = > > user2-grps = > > userint1 = 0 > > userint2 = 0 > > userint3 = 0 > > userint4 = 0 > > userreal1= 0 > > userreal2= 0 > > userreal3= 0 > > userreal4= 0 > > > > With Best Regards, > > Kalyanashis Jana > > > > On Wed, Oct 5, 2016 at 4:18 PM, Mark Abraham > > wrote: > > > > > Hi, > > > > > > "It has been abnormally terminated" is too vague to lead to effective > > help. > > > What did the terminal and log files say about what led to termination? > > > > > > Mark > > > > > > On Wed, Oct 5, 2016 at 12:43 PM Kalyanashis Jana < > > kalyan.chem...@gmail.com > > > > > > > wrote: > > > > > > > Dear Sotirios, > > > > Thank you very much for your reply. I have used ΔΤ=10 K, 5K and > 3K... > > > But > > > > it has been abnormally termina
Re: [gmx-users] Replica Exchange MD
t; constraint-algorithm = Lincs > continuation = no > Shake-SOR= no > shake-tol= 0.0001 > lincs-order = 4 > lincs-iter = 1 > lincs-warnangle = 30 > morse= no > energygrp-excl = > nwall= 0 > wall-type= 9-3 > wall-r-linpot= -1 > wall-atomtype= > wall-density = > wall-ewald-zfac = 3 > pull = no > ;rotation = no > disre= No > disre-weighting = Conservative > disre-mixed = no > disre-fc = 1000 > disre-tau= 0 > nstdisreout = 100 > orire= no > orire-fc = 0 > orire-tau= 0 > orire-fitgrp = > nstorireout = 100 > free-energy = no > couple-moltype = > couple-lambda0 = vdw-q > couple-lambda1 = vdw-q > couple-intramol = no > init-lambda = -1 > ;init-lambda-state= -1 > delta-lambda = 0 > nstdhdl = 50 > fep-lambdas = > mass-lambdas = > coul-lambdas = > vdw-lambdas = > bonded-lambdas = > restraint-lambdas= > temperature-lambdas = > ;calc-lambda-neighbors= 1 > init-lambda-weights = > ;dhdl-print-energy= no > sc-alpha = 0 > sc-power = 1 > ;sc-r-power = 6 > sc-sigma = 0.3 > ;sc-coul = no > separate-dhdl-file = yes > dhdl-derivatives = yes > dh_hist_size = 0 > dh_hist_spacing = 0.1 > acc-grps = > accelerate = > freezegrps = > freezedim= > cos-acceleration = 0 > deform = > ;simulated-tempering = no > ;simulated-tempering-scaling = geometric > ;sim-temp-low = 300 > ;sim-temp-high= 300 > E-x = > E-xt = > E-y = > E-yt = > E-z = > E-zt = > ;adress = no > user1-grps = > user2-grps = > userint1 = 0 > userint2 = 0 > userint3 = 0 > userint4 = 0 > userreal1= 0 > userreal2= 0 > userreal3= 0 > userreal4= 0 > > With Best Regards, > Kalyanashis Jana > > On Wed, Oct 5, 2016 at 4:18 PM, Mark Abraham > wrote: > > > Hi, > > > > "It has been abnormally terminated" is too vague to lead to effective > help. > > What did the terminal and log files say about what led to termination? > > > > Mark > > > > On Wed, Oct 5, 2016 at 12:43 PM Kalyanashis Jana < > kalyan.chem...@gmail.com > > > > > wrote: > > > > > Dear Sotirios, > > > Thank you very much for your reply. I have used ΔΤ=10 K, 5K and 3K... > > But > > > it has been abnormally terminated. > > > Is there any possible solution? Please help me... > > > Thanks in advance, > > > Kalyanashis > > > > > > On Wed, Oct 5, 2016 at 12:02 PM, Sotirios Dionysios I. Papadatos < > > > si.papada...@edu.cut.ac.cy> wrote: > > > > > > > In this case maybe, just maybe there is a big gap between > temperatures. > > > > Hence the ΔΕ is to large and the exchange destabilizes your system. > > Try a > > > > dummy run with a small ΔΤ to see if this is the case > > > > > > > > > > > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < > > > > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of > > > > Kalyanashis Jana > > > > Sent: Tuesday, October 4, 2016 9:40:08 PM > > > > To: Discussion list for GROMACS users > > > > Subject: [gmx-users] Replica Exchange MD > > > > > > > > Dear all, > > > > I am trying to perform a REMD simulation for a protein drug complex. > I > > > have > > > > followed REMD tutorial ( > > > > http://www.gromacs.org/Documentation/Tutorials/ > > GROMACS_USA_Workshop_and_ > > > > Conference_2013/An_introduction_to_replica_ > > exchange_simulations%3A_Mark_ > > > >
Re: [gmx-users] Replica Exchange MD
= vdw-lambdas = bonded-lambdas = restraint-lambdas= temperature-lambdas = ;calc-lambda-neighbors= 1 init-lambda-weights = ;dhdl-print-energy= no sc-alpha = 0 sc-power = 1 ;sc-r-power = 6 sc-sigma = 0.3 ;sc-coul = no separate-dhdl-file = yes dhdl-derivatives = yes dh_hist_size = 0 dh_hist_spacing = 0.1 acc-grps = accelerate = freezegrps = freezedim= cos-acceleration = 0 deform = ;simulated-tempering = no ;simulated-tempering-scaling = geometric ;sim-temp-low = 300 ;sim-temp-high= 300 E-x = E-xt = E-y = E-yt = E-z = E-zt = ;adress = no user1-grps = user2-grps = userint1 = 0 userint2 = 0 userint3 = 0 userint4 = 0 userreal1= 0 userreal2= 0 userreal3= 0 userreal4= 0 With Best Regards, Kalyanashis Jana On Wed, Oct 5, 2016 at 4:18 PM, Mark Abraham wrote: > Hi, > > "It has been abnormally terminated" is too vague to lead to effective help. > What did the terminal and log files say about what led to termination? > > Mark > > On Wed, Oct 5, 2016 at 12:43 PM Kalyanashis Jana > > wrote: > > > Dear Sotirios, > > Thank you very much for your reply. I have used ΔΤ=10 K, 5K and 3K... > But > > it has been abnormally terminated. > > Is there any possible solution? Please help me... > > Thanks in advance, > > Kalyanashis > > > > On Wed, Oct 5, 2016 at 12:02 PM, Sotirios Dionysios I. Papadatos < > > si.papada...@edu.cut.ac.cy> wrote: > > > > > In this case maybe, just maybe there is a big gap between temperatures. > > > Hence the ΔΕ is to large and the exchange destabilizes your system. > Try a > > > dummy run with a small ΔΤ to see if this is the case > > > > > > > > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < > > > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of > > > Kalyanashis Jana > > > Sent: Tuesday, October 4, 2016 9:40:08 PM > > > To: Discussion list for GROMACS users > > > Subject: [gmx-users] Replica Exchange MD > > > > > > Dear all, > > > I am trying to perform a REMD simulation for a protein drug complex. I > > have > > > followed REMD tutorial ( > > > http://www.gromacs.org/Documentation/Tutorials/ > GROMACS_USA_Workshop_and_ > > > Conference_2013/An_introduction_to_replica_ > exchange_simulations%3A_Mark_ > > > Abraham,_Session_1B > > > ). > > > I have prepared 10 set for the REMD simulation and generated the tpr > file > > > for MD run. I have used "mpirun -np 10 mdrun_mpi -v -multidir > > > equil[0123456789 <0123-45%2067%2089>]" for MD run. It has been > > abnormally terminated at the > > > middle of the MD run. However, the same topol.tpr files have produced > > > normally terminated MD run when the simulations have been run > > > individually using > > > "mpirun -np 10 mdrun_mpi -v -s topol.tpr " > > > Please suggest me, how can I overcome this problem. > > > Looking forward to hear from you. > > > > > > > > > Thanks in advance, > > > Kalyanashis Jana > > > > > > > > > -- > > > Thanks with regards > > > Kalyanashis Jana > > > -- > > > 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
Re: [gmx-users] Replica Exchange MD
Hi, "It has been abnormally terminated" is too vague to lead to effective help. What did the terminal and log files say about what led to termination? Mark On Wed, Oct 5, 2016 at 12:43 PM Kalyanashis Jana wrote: > Dear Sotirios, > Thank you very much for your reply. I have used ΔΤ=10 K, 5K and 3K... But > it has been abnormally terminated. > Is there any possible solution? Please help me... > Thanks in advance, > Kalyanashis > > On Wed, Oct 5, 2016 at 12:02 PM, Sotirios Dionysios I. Papadatos < > si.papada...@edu.cut.ac.cy> wrote: > > > In this case maybe, just maybe there is a big gap between temperatures. > > Hence the ΔΕ is to large and the exchange destabilizes your system. Try a > > dummy run with a small ΔΤ to see if this is the case > > > > > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < > > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of > > Kalyanashis Jana > > Sent: Tuesday, October 4, 2016 9:40:08 PM > > To: Discussion list for GROMACS users > > Subject: [gmx-users] Replica Exchange MD > > > > Dear all, > > I am trying to perform a REMD simulation for a protein drug complex. I > have > > followed REMD tutorial ( > > http://www.gromacs.org/Documentation/Tutorials/GROMACS_USA_Workshop_and_ > > Conference_2013/An_introduction_to_replica_exchange_simulations%3A_Mark_ > > Abraham,_Session_1B > > ). > > I have prepared 10 set for the REMD simulation and generated the tpr file > > for MD run. I have used "mpirun -np 10 mdrun_mpi -v -multidir > > equil[0123456789 <0123-45%2067%2089>]" for MD run. It has been > abnormally terminated at the > > middle of the MD run. However, the same topol.tpr files have produced > > normally terminated MD run when the simulations have been run > > individually using > > "mpirun -np 10 mdrun_mpi -v -s topol.tpr " > > Please suggest me, how can I overcome this problem. > > Looking forward to hear from you. > > > > > > Thanks in advance, > > Kalyanashis Jana > > > > > > -- > > Thanks with regards > > Kalyanashis Jana > > -- > > 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. > > > > > -- > Thanks with regards > Kalyanashis Jana > -- > 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] Replica Exchange MD
Dear Sotirios, Thank you very much for your reply. I have used ΔΤ=10 K, 5K and 3K... But it has been abnormally terminated. Is there any possible solution? Please help me... Thanks in advance, Kalyanashis On Wed, Oct 5, 2016 at 12:02 PM, Sotirios Dionysios I. Papadatos < si.papada...@edu.cut.ac.cy> wrote: > In this case maybe, just maybe there is a big gap between temperatures. > Hence the ΔΕ is to large and the exchange destabilizes your system. Try a > dummy run with a small ΔΤ to see if this is the case > > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of > Kalyanashis Jana > Sent: Tuesday, October 4, 2016 9:40:08 PM > To: Discussion list for GROMACS users > Subject: [gmx-users] Replica Exchange MD > > Dear all, > I am trying to perform a REMD simulation for a protein drug complex. I have > followed REMD tutorial ( > http://www.gromacs.org/Documentation/Tutorials/GROMACS_USA_Workshop_and_ > Conference_2013/An_introduction_to_replica_exchange_simulations%3A_Mark_ > Abraham,_Session_1B > ). > I have prepared 10 set for the REMD simulation and generated the tpr file > for MD run. I have used "mpirun -np 10 mdrun_mpi -v -multidir > equil[0123456789]" for MD run. It has been abnormally terminated at the > middle of the MD run. However, the same topol.tpr files have produced > normally terminated MD run when the simulations have been run > individually using > "mpirun -np 10 mdrun_mpi -v -s topol.tpr " > Please suggest me, how can I overcome this problem. > Looking forward to hear from you. > > > Thanks in advance, > Kalyanashis Jana > > > -- > Thanks with regards > Kalyanashis Jana > -- > 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. -- Thanks with regards Kalyanashis Jana -- 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] Replica Exchange MD
In this case maybe, just maybe there is a big gap between temperatures. Hence the ΔΕ is to large and the exchange destabilizes your system. Try a dummy run with a small ΔΤ to see if this is the case From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Kalyanashis Jana Sent: Tuesday, October 4, 2016 9:40:08 PM To: Discussion list for GROMACS users Subject: [gmx-users] Replica Exchange MD Dear all, I am trying to perform a REMD simulation for a protein drug complex. I have followed REMD tutorial ( http://www.gromacs.org/Documentation/Tutorials/GROMACS_USA_Workshop_and_Conference_2013/An_introduction_to_replica_exchange_simulations%3A_Mark_Abraham,_Session_1B ). I have prepared 10 set for the REMD simulation and generated the tpr file for MD run. I have used "mpirun -np 10 mdrun_mpi -v -multidir equil[0123456789]" for MD run. It has been abnormally terminated at the middle of the MD run. However, the same topol.tpr files have produced normally terminated MD run when the simulations have been run individually using "mpirun -np 10 mdrun_mpi -v -s topol.tpr " Please suggest me, how can I overcome this problem. Looking forward to hear from you. Thanks in advance, Kalyanashis Jana -- Thanks with regards Kalyanashis Jana -- 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] Replica Exchange MD
Dear all, I am trying to perform a REMD simulation for a protein drug complex. I have followed REMD tutorial ( http://www.gromacs.org/Documentation/Tutorials/GROMACS_USA_Workshop_and_Conference_2013/An_introduction_to_replica_exchange_simulations%3A_Mark_Abraham,_Session_1B ). I have prepared 10 set for the REMD simulation and generated the tpr file for MD run. I have used "mpirun -np 10 mdrun_mpi -v -multidir equil[0123456789]" for MD run. It has been abnormally terminated at the middle of the MD run. However, the same topol.tpr files have produced normally terminated MD run when the simulations have been run individually using "mpirun -np 10 mdrun_mpi -v -s topol.tpr " Please suggest me, how can I overcome this problem. Looking forward to hear from you. Thanks in advance, Kalyanashis Jana -- Thanks with regards Kalyanashis Jana -- 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] Replica Exchange MD
Dear GMX Users, I am trying to apply the REMD to study the difference between the folding free energy of a 24 residue peptide with two different conformations. As I am short of required number of processors for REMD in explicit water, I am trying my luck with implicit solvent. I have come across many papers that have used implicit solvent in their simulation studies. So, after various trails of temp. distributions, I selected some 15 replicas with the following temp. range: Repl 0 1 2 3 4 5 6 7 8 910 11121314 Repl T 250.0 264.0 279.0 295.0 312.0 329.0 348.0 367.0 388.0 410.0 433.0 458.0 484.0 511.0 540.0 Repl Repl exchange interval: 1000 Here's the result for a trial run of 2ns per replica: Replica exchange statistics Repl 999 attempts, 500 odd, 499 even Repl average probabilities: Repl 0123456789 10 11 12 13 14 Repl .34 .34 .21 .27 .39 .41 .40 .37 .41 .42 .41 .43 .46 .44 Repl number of exchanges: Repl 0123456789 10 11 12 13 14 Repl 166 155 116 130 184 201 193 185 212 216 200 208 223 225 Repl average number of exchanges: Repl 0123456789 10 11 12 13 14 Repl .33 .31 .23 .26 .37 .40 .39 .37 .42 .43 .40 .42 .45 .45 The average exchange ratio for each replica lies between 0.3-0.4. Is it okay ? . As the value between 0.2-0.3 is considered to be good. Here's the graph for replica_index , replica_temp and PE of replicas. https://www.dropbox.com/s/dykxwwqulpfpw8x/REMD.png I want to know whether, I can move forward with the large production runs or not ?? Pls respond - Bharat -- 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] Replica Exchange MD
Dear GMX Users, I am trying to apply the REMD to study the difference between the folding free energy of a 24 residue peptide with two different conformations. As I am short of required number of processors for REMD in explicit water, I am trying my luck with implicit solvent. I have come across many papers that have used implicit solvent in their simulation studies. So, after various trails of temp. distributions, I selected some 15 replicas with the following temp. range: Repl 0 1 2 3 4 5 6 7 8 910 11121314 Repl T 250.0 264.0 279.0 295.0 312.0 329.0 348.0 367.0 388.0 410.0 433.0 458.0 484.0 511.0 540.0 Repl Repl exchange interval: 1000 Here's the result for a trial run of 2ns per replica: Replica exchange statistics Repl 999 attempts, 500 odd, 499 even Repl average probabilities: Repl 0123456789 10 11 12 13 14 Repl .34 .34 .21 .27 .39 .41 .40 .37 .41 .42 .41 .43 .46 .44 Repl number of exchanges: Repl 0123456789 10 11 12 13 14 Repl 166 155 116 130 184 201 193 185 212 216 200 208 223 225 Repl average number of exchanges: Repl 0123456789 10 11 12 13 14 Repl .33 .31 .23 .26 .37 .40 .39 .37 .42 .43 .40 .42 .45 .45 The average exchange ratio for each replica lies between 0.3-0.4. Is it okay ? . As the value between 0.2-0.3 is considered to be good. Here's the graph for replica_index , replica_temp and PE of replicas. https://www.dropbox.com/s/dykxwwqulpfpw8x/REMD.png I want to know whether, I can move forward with the large production runs or not ?? Pls respond - Bharat -- 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.
