RE: [gmx-users] Re: boundaries in PMF
OK, however, just one point about your last comment: > I suspect this is why g_wham is finding a range of values only equal to half > of > your expected reaction coordinate; it is considering only the positive > displacement along the reaction coordinate. It seems like all the channel is explored, not only one half. If g_wham was only considering the positive displacement I should see a profile for just one half of the channel, shouldn´t I? and I can see a profile typical for the entire channel. Rebeca. > Date: Thu, 31 May 2012 15:42:06 -0400 > From: jalem...@vt.edu > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] Re: boundaries in PMF > > > > On 5/31/12 3:37 PM, Rebeca García Fandiño wrote: > > Hi, > > the center of mass of my channel is at the middle of the ion channel, and > > it is > > a symmetric system, so I suppose these results would be OK. Anyway, I will > > check > > the options you propose. > > If you are sampling regions above and below the channel/membrane, then the > "distance" geometry is not appropriate; you need either "direction" or > (perhaps > the most flexible option) "position." There are a number of useful > discussions > on such topics in the list archive and in my umbrella sampling tutorial for > you > to consider. You can likely create a series of .tpr files from new .mdp > files > with correct options to run the analysis. > > I suspect this is why g_wham is finding a range of values only equal to half > of > your expected reaction coordinate; it is considering only the positive > displacement along the reaction coordinate. > > -Justin > > > Thanks a lot for all your comments!! > > Best wishes, > > Rebeca. > > > > > Date: Thu, 31 May 2012 20:08:26 +0200 > > > From: schl...@uni-mainz.de > > > To: gmx-users@gromacs.org > > > Subject: [gmx-users] Re: boundaries in PMF > > > > > > Where is the center of mass of reference group (MOL) located? > > > > > > It seems that the COM is near the middle of the ion channel. Since you > > > use 'pull_geometry=distance', g_wham will look only for the distance > > > between 'MOL' and 'Na' and that leads to problem. > > > If the com of 'MOL' sits in the center of the channel (which is around > > > 5nm long), one has 2.5nm in both directions. Since g_wham uses only the > > > distance you get the PMF for half of the channel, but with the data of > > > both parts. > > > If the channel would be symmetric and the com of 'MOL' would lie exactly > > > in the middle of the channel, this could be ok. But if even one of both > > > assumptions is wrong, the results would be errorous. > > > > > > A better approach would be to use 'pull_geometry=direction', since the > > > you define a vector along which the windows lie and do not have the > > > problem that the distance is in both directions (along positive and > > > negative vector) the same. > > > Only problem could be that g_wham supports 'pull_geometry=direction' > > > only from gromacs 4.5.x (don't know this, since instead of umbrella > > > smapling i use thermodynamik integration, where one uses constraints > > > (instead of restraints) and integrates the constraint-force; but the > > > conceptual problem with 'distance/direction' is the same). > > > > > > Another approach (with 'pull_geometry=distance') would be to use a > > > reference group which is just outside of the channel (like going some > > > steps away from the channel, along the vector which goes through the > > > channel). If there is only water, it would be bad, because then the > > > reference group would be move away. > > > But then on could use the entry and exit of the channel as a reference > > > point for two simulations. In the case that the entry is the reference > > > group, the PMF would be ill defined near the entry, but from the > > > simulation with the exit as reference you would get the right PMF for > > > the entry region and vice versa. > > > > > > Greetings > > > Thomas > > > > > > > > > Am 31.05.2012 19:39, schrieb gmx-users-requ...@gromacs.org: > > > > Thanks a lot for your quick answer. The mdp file I have used is copied > > > > below. What is strange is that when I look at the *gro files for the > > > > different windows (100 windows
RE: [gmx-users] Re: boundaries in PMF
Yes, my profile seems normal, the only problem are the units in the x-axis, because I expected them to be in the range of the dimensions of the channel. I will try if I see differences with the other options you proposed, anyway. Thanks a lot for your help!! Best wishes, Rebeca. > Date: Thu, 31 May 2012 15:52:48 -0400 > From: jalem...@vt.edu > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] Re: boundaries in PMF > > > > On 5/31/12 3:51 PM, Rebeca García Fandiño wrote: > > OK, > > however, just one point about your last comment: > > > > > I suspect this is why g_wham is finding a range of values only equal to > > half of > > > your expected reaction coordinate; it is considering only the positive > > > displacement along the reaction coordinate. > > > > It seems like all the channel is explored, not only one half. If g_wham was > > only > > considering the positive displacement I should see a profile for just one > > half > > of the channel, shouldn´t I? and I can see a profile typical for the entire > > channel. > > > > Then perhaps it's just a small g_wham output bug (boundary values). You > didn't > mention that your profile looked normal ;) > > -Justin > > -- > > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] Re: boundaries in PMF
Hi, the center of mass of my channel is at the middle of the ion channel, and it is a symmetric system, so I suppose these results would be OK. Anyway, I will check the options you propose. Thanks a lot for all your comments!! Best wishes, Rebeca. > Date: Thu, 31 May 2012 20:08:26 +0200 > From: schl...@uni-mainz.de > To: gmx-users@gromacs.org > Subject: [gmx-users] Re: boundaries in PMF > > Where is the center of mass of reference group (MOL) located? > > It seems that the COM is near the middle of the ion channel. Since you > use 'pull_geometry=distance', g_wham will look only for the distance > between 'MOL' and 'Na' and that leads to problem. > If the com of 'MOL' sits in the center of the channel (which is around > 5nm long), one has 2.5nm in both directions. Since g_wham uses only the > distance you get the PMF for half of the channel, but with the data of > both parts. > If the channel would be symmetric and the com of 'MOL' would lie exactly > in the middle of the channel, this could be ok. But if even one of both > assumptions is wrong, the results would be errorous. > > A better approach would be to use 'pull_geometry=direction', since the > you define a vector along which the windows lie and do not have the > problem that the distance is in both directions (along positive and > negative vector) the same. > Only problem could be that g_wham supports 'pull_geometry=direction' > only from gromacs 4.5.x (don't know this, since instead of umbrella > smapling i use thermodynamik integration, where one uses constraints > (instead of restraints) and integrates the constraint-force; but the > conceptual problem with 'distance/direction' is the same). > > Another approach (with 'pull_geometry=distance') would be to use a > reference group which is just outside of the channel (like going some > steps away from the channel, along the vector which goes through the > channel). If there is only water, it would be bad, because then the > reference group would be move away. > But then on could use the entry and exit of the channel as a reference > point for two simulations. In the case that the entry is the reference > group, the PMF would be ill defined near the entry, but from the > simulation with the exit as reference you would get the right PMF for > the entry region and vice versa. > > Greetings > Thomas > > > Am 31.05.2012 19:39, schrieb gmx-users-requ...@gromacs.org: > > Thanks a lot for your quick answer. The mdp file I have used is copied > > below. What is strange is that when I look at the *gro files for the > > different windows (100 windows in total), i. e: window 1: 8704Na Na56458 > > 5.134 5.085 5.824 window 50: 8704Na Na56458 5.053 5.081 3.459 window > > 100: 8704Na Na56458 4.990 5.042 0.951 you can see that the z-coordinate > > goes from 0.951 to 5.824 nm I should have a total distance in the x-axis > > of about 5 nm, and however, the boundaries calculated by g_wham are > > "Determined boundaries to 0.35 to 2.603290 " Can you see anything in > > the mdp file which is causing this behaviour...? Thanks again for your > > help! MDP FILE USED: title = Umbrella pulling simulation define = > > -DPOSRES_B define = ; Run parameters integrator = md dt = 0.002 tinit = > > 0 nsteps = 50 ; 1 ns nstcomm = 10 ; Output parameters nstxout = 5000 > > ; every 10 ps nstvout = 5000 nstfout = 5000 nstxtcout = 5000 ; every 10 > > ps nstenergy = 5000 ; Bond parameters constraint_algorithm = lincs > > constraints = all-bonds continuation = yes ; Single-range cutoff scheme > > nstlist = 5 ns_type = grid rlist = 1.4 rcoulomb = 1.4 rvdw = 1.4 ; PME > > electrostatics parameters coulombtype = PME fourierspacing = 0.12 > > fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = > > 1e-5 optimize_fft = yes ;Berendsen temperature coupling is on Tcoupl = > > V-rescale tau_t = 0.1 0.1 0.1 tc-grps = MOL dop WAT_Cl_Na ref_t = 300 > > 300 300 ; Pressure coupling Pcoupl = Parrinello-Rahman Pcoupltype = > > Semiisotropic ; Time constant (ps), compressibility (1/bar) and > > reference P (bar) tau-p = 1.0 1.0 compressibility = 4.6E-5 4.6E-5 ref-p > > = 1.0 1.0 ; Generate velocities is off gen_vel = no ; Periodic boundary > > conditions are on in all directions pbc = xyz ; Long-range dispersion > > correction DispCorr = EnerPres ; Pull code pull = umbrella pull_geometry > > = distance pull_dim = N N Y pull_start = yes pull_ngroups = 1 > > pull_group0 = MOL pull_group1 = Na pull_init1 = 0 pull_rate1 = 0.0 > > pull_k1 = 1000 ; kJ mol^-1 nm^-2 pull_nstxout = 1000 ; every 2 ps > > pull_nstfout = 1000 ; every 2 ps > >> > Date: Thu, 31 May 2012 13:25:26 -0400 > >> > From:jalem...@vt.edu > >> > To:gmx-users@gromacs.org > >> > Subject: Re: [gmx-users] boundaries in PMF > >> > > >> > > >> > > >> > On 5/31/12 1:20 PM, Rebeca Garc?a Fandi?o wrote: > >>> > > Hi, > >>> > > I am trying to calculate a PMF for an ion along a channel. > >>> > Everything went OK, > >>> > > but when I u
RE: [gmx-users] boundaries in PMF
Thanks again, and sorry for insisting, but I am not sure of understanding it totally. So, the boundaries g_wham calculates are not related to the dimensions of my channel? Would be any way to convert these units into the position of the ion in the channel in each case? Thanks again a lot for your help. Best wishes, Rebeca. > Date: Thu, 31 May 2012 13:45:18 -0400 > From: jalem...@vt.edu > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] boundaries in PMF > > > > On 5/31/12 1:38 PM, Rebeca García Fandiño wrote: > > Thanks a lot for your quick answer. > > The mdp file I have used is copied below. What is strange is that when I > > look at > > the *gro files for the different windows (100 windows in total), i. e: > > > > window 1: 8704Na Na56458 5.134 5.085 5.824 > > window 50: 8704Na Na56458 5.053 5.081 3.459 > > window 100: 8704Na Na56458 4.990 5.042 0.951 > > > > you can see that the z-coordinate goes from 0.951 to 5.824 nm > > > > I should have a total distance in the x-axis of about 5 nm, and however, the > > boundaries calculated by g_wham are > > > > "Determined boundaries to 0.35 to 2.603290 " > > > > Can you see anything in the mdp file which is causing this behaviour...? > > > > No, but you need to be careful how you're interpreting what you get. The > z-coordinate of your ion is not what's relevant; its displacement along the > z-axis from the reference group is what matters. So unless your reference > group > is centered at z=0 (which it shouldn't, based on the way Gromacs builds > boxes), > you won't have a range equivalent to the z-coordinate. The output of grompp > states what the restraint distance is in all cases, based on the coordinates > and > dimensions chosen for the restraint. > > -Justin > > > Thanks again for your help! > > > > > > > > > > MDP FILE USED: > > title = Umbrella pulling simulation > > define = -DPOSRES_B > > define = > > ; Run parameters > > integrator = md > > dt = 0.002 > > tinit = 0 > > nsteps = 50 ; 1 ns > > nstcomm = 10 > > ; Output parameters > > nstxout = 5000 ; every 10 ps > > nstvout = 5000 > > nstfout = 5000 > > nstxtcout = 5000 ; every 10 ps > > nstenergy = 5000 > > ; Bond parameters > > constraint_algorithm = lincs > > constraints = all-bonds > > continuation = yes > > ; Single-range cutoff scheme > > nstlist = 5 > > ns_type = grid > > rlist = 1.4 > > rcoulomb = 1.4 > > rvdw = 1.4 > > ; PME electrostatics parameters > > coulombtype = PME > > fourierspacing = 0.12 > > fourier_nx = 0 > > fourier_ny = 0 > > fourier_nz = 0 > > pme_order = 4 > > ewald_rtol = 1e-5 > > optimize_fft = yes > > ;Berendsen temperature coupling is on > > Tcoupl = V-rescale > > tau_t = 0.1 0.1 0.1 > > tc-grps = MOL dop WAT_Cl_Na > > ref_t = 300 300 300 > > ; Pressure coupling > > Pcoupl = Parrinello-Rahman > > Pcoupltype = Semiisotropic > > ; Time constant (ps), compressibility (1/bar) and reference P (bar) > > tau-p = 1.0 1.0 > > compressibility = 4.6E-5 4.6E-5 > > ref-p = 1.0 1.0 > > ; Generate velocities is off > > gen_vel = no > > ; Periodic boundary conditions are on in all directions > > pbc = xyz > > ; Long-range dispersion correction > > DispCorr = EnerPres > > ; Pull code > > pull = umbrella > > pull_geometry = distance > > pull_dim = N N Y > > pull_start = yes > > pull_ngroups = 1 > > pull_group0 = MOL > > pull_group1 = Na > > pull_init1 = 0 > > pull_rate1 = 0.0 > > pull_k1 = 1000 ; kJ mol^-1 nm^-2 > > pull_nstxout = 1000 ; every 2 ps > > pull_nstfout = 1000 ; every 2 ps > > > > > > > > > > > > > > > > > > > > > Date: Thu, 31 May 2012 13:25:26 -0400 > > > From: jalem...@vt.edu > > > To: gmx-users@gromacs.org > > > Subject: Re: [gmx-users] boundaries in PMF > > > > > > > > > > > > On 5/31/12 1:20 PM, Rebeca García Fandiño wrote: > > > > Hi, > > > > I am trying to calculate a PMF for an ion along a channel. Everything > > went OK, > > > > but when I used g_wham I got a profile with strange dimensions for the > > x-axis. > > > > What are the boundaries g_wham is using for calculating the units of > > x-axis? > > > > > > > > > > The values are based on the restraint distances along the reactio
RE: [gmx-users] boundaries in PMF
Thanks a lot for your quick answer. The mdp file I have used is copied below. What is strange is that when I look at the *gro files for the different windows (100 windows in total), i. e: window 1: 8704Na Na56458 5.134 5.085 5.824 window 50: 8704Na Na56458 5.053 5.081 3.459 window 100: 8704Na Na56458 4.990 5.042 0.951 you can see that the z-coordinate goes from 0.951 to 5.824 nm I should have a total distance in the x-axis of about 5 nm, and however, the boundaries calculated by g_wham are "Determined boundaries to 0.35 to 2.603290 " Can you see anything in the mdp file which is causing this behaviour...? Thanks again for your help! MDP FILE USED: title = Umbrella pulling simulation define = -DPOSRES_B define = ; Run parameters integrator = md dt = 0.002 tinit = 0 nsteps = 50 ; 1 ns nstcomm = 10 ; Output parameters nstxout = 5000 ; every 10 ps nstvout = 5000 nstfout = 5000 nstxtcout = 5000 ; every 10 ps nstenergy = 5000 ; Bond parameters constraint_algorithm= lincs constraints = all-bonds continuation= yes ; Single-range cutoff scheme nstlist = 5 ns_type = grid rlist = 1.4 rcoulomb= 1.4 rvdw= 1.4 ; PME electrostatics parameters coulombtype = PME fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft= yes ;Berendsen temperature coupling is on Tcoupl = V-rescale tau_t = 0.1 0.10.1 tc-grps = MOL dop WAT_Cl_Na ref_t = 300 300300 ; Pressure coupling Pcoupl = Parrinello-Rahman Pcoupltype = Semiisotropic ; Time constant (ps), compressibility (1/bar) and reference P (bar) tau-p= 1.0 1.0 compressibility = 4.6E-5 4.6E-5 ref-p= 1.0 1.0 ; Generate velocities is off gen_vel = no ; Periodic boundary conditions are on in all directions pbc = xyz ; Long-range dispersion correction DispCorr= EnerPres ; Pull code pull= umbrella pull_geometry = distance pull_dim= N N Y pull_start = yes pull_ngroups= 1 pull_group0 = MOL pull_group1 = Na pull_init1 = 0 pull_rate1 = 0.0 pull_k1 = 1000 ; kJ mol^-1 nm^-2 pull_nstxout= 1000 ; every 2 ps pull_nstfout= 1000 ; every 2 ps > Date: Thu, 31 May 2012 13:25:26 -0400 > From: jalem...@vt.edu > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] boundaries in PMF > > > > On 5/31/12 1:20 PM, Rebeca García Fandiño wrote: > > Hi, > > I am trying to calculate a PMF for an ion along a channel. Everything went > > OK, > > but when I used g_wham I got a profile with strange dimensions for the > > x-axis. > > What are the boundaries g_wham is using for calculating the units of x-axis? > > > > The values are based on the restraint distances along the reaction coordinate. > > > I have used: > > g_wham -it tpr-files.dat -if pullf-files.dat -o file_output.xvg -hist > > file_histo_output.xvg -unit kCal -cycl yes > > > > (version 4.0.7) > > > > and the units I got in the x-axis are determined by the boundaries: > > > > "Determined boundaries to 0.35 to 2.603290 " > > > > Which are these units? nm? > > > > Yes. > > > The z coordinate for my ion explores at least 5 nm!! > > > > I am a bit confused about that. > > > > The exact output depends on how you set up the umbrella sampling (in the .mdp > file). The range of values corresponds to whatever the distances are that > are > sampled in the various windows. Perhaps there is a sign issue here? Do you > have some restraints that are at negative displacement and others at > positive? > Did you set up the .mdp files properly to account for this behavior? > > -Justin > > -- > > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-use
[gmx-users] boundaries in PMF
Hi, I am trying to calculate a PMF for an ion along a channel. Everything went OK, but when I used g_wham I got a profile with strange dimensions for the x-axis. What are the boundaries g_wham is using for calculating the units of x-axis? I have used: g_wham -it tpr-files.dat -if pullf-files.dat -o file_output.xvg -hist file_histo_output.xvg -unit kCal -cycl yes (version 4.0.7) and the units I got in the x-axis are determined by the boundaries: "Determined boundaries to 0.35 to 2.603290 " Which are these units? nm? The z coordinate for my ion explores at least 5 nm!! I am a bit confused about that. Any help will be appreciated. Thanks a lot for your help in advance! Best wishes, Dr.Rebeca Garcia Santiago de Compostela University Spain -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] deformations aplying an electric field
Hi, I am trying to simulate a nanotube inserted into a lipid bilayer using Gromacs 4, applying an external electric field (in the direction of the z axis). I have added this line to my input file: ;Electric field E_z = 1 1.0 0 The calculations finish without problem, however I can see a big deformation both of the nanotube and also of the membrane. Is this normal? When I use a smaller electric field: E_z = 1 0.01 0 I cannot see these deformations. Is it usual to find deformations using high electric fields such as 1V? Thanks a lot in advance. Best wishes, Dr. Rebeca Garcia Santiago de Compostela University Spain -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] analysis of PMF calculations
Thanks, Justin. Just one note: the values of min and max are not the same (-min -2.4750 -max 2.4750), they have opposite values. The c.o.m is taken as zero. If they were the same I would understand your suggestion, but they are not, so Gromacs should not understand that the system has zero size, should it? Rebeca. > Date: Sun, 11 Sep 2011 17:39:55 -0400 > From: jalem...@vt.edu > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] analysis of PMF calculations > > > > Rebeca García Fandiño wrote: > > Thanks again, I have uploaded to the version 4.5.4 and instead of zeros > > in the second column, I obtain nan, which comes to be the same :-S > > Sorry, but I am a bit confused about your comments. If I use the option > > -cycl (this is what I can read in the Help from Gromacs): > > > > "For cyclic or periodic reaction coordinates (dihedral angle, channel PMF > > without osmotic gradient), the option -cycl is useful. g_wham will make use > > of the periodicity of the system and generate a periodic PMF. The first and > > the last bin of the reaction coordinate will assumed be be neighbors." > > > > If I assume that my channel is periodic (which it is not), I do not get > > errors. The problem comes if I assume that it is not periodic, then my > > second column is "nan". In a previous mail, you had wrote me: > > > > In what way is your channel not periodic? I'm trying to understand your > problem > more completely. I would suspect your issue (judging by previous commands) > is > that if the value of max and min are the same in the absence of -cycl, then > you'll get nonsense as output. Hence I said: > > >> That makes sense. You're telling g_wham that you have a PMF starting > >> and ending at the same place, but it's not a periodic profile. It can't > >> debias the sampling windows over zero space. > > > > > > So, just to get it clear, if I assume that a system that itś not > > periodic is periodic (using the option -cycl), I should have problems, > > and not the opposite, what itś just what I am observing. Is it not right? > > I still need to know why your system isn't periodic. From before, using max > = > min in conjunction with -cycl gives g_wham a reasonable set of parameters to > work with. Having max = min without -cycl is going to fail, because > essentially > you're telling g_wham that the system has zero size and therefore the > reaction > coordinate is of zero length (which is why, I suspect, you get "nan" - > division > by zero). > > > Besides, I have also analyzed analogous PMF results using the same > > channel, but another ion (the PMF is for an ion crossing a membrane > > channel), and I do not have this type of problem. > > > > From this description, you should indeed have a periodic PMF. Thus I don't > understand the insistence that -cycl shouldn't be used. > > -Justin > > -- > > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] analysis of PMF calculations
Thanks again, I have uploaded to the version 4.5.4 and instead of zeros in the second column, I obtain nan, which comes to be the same :-S Sorry, but I am a bit confused about your comments. If I use the option -cycl (this is what I can read in the Help from Gromacs): "For cyclic or periodic reaction coordinates (dihedral angle, channel PMF without osmotic gradient), the option -cycl is useful. g_wham will make use of the periodicity of the system and generate a periodic PMF. The first and the last bin of the reaction coordinate will assumed be be neighbors." If I assume that my channel is periodic (which it is not), I do not get errors. The problem comes if I assume that it is not periodic, then my second column is "nan". In a previous mail, you had wrote me: > That makes sense. You're telling g_wham that you have a PMF starting > and ending at the same place, but it's not a periodic profile. It can't > debias the sampling windows over zero space. So, just to get it clear, if I assume that a system that itś not periodic is periodic (using the option -cycl), I should have problems, and not the opposite, what itś just what I am observing. Is it not right? Besides, I have also analyzed analogous PMF results using the same channel, but another ion (the PMF is for an ion crossing a membrane channel), and I do not have this type of problem. Sorry for insisting, but I did not understand it :-S Thanks a lot for your help. Best wishes, Rebeca. > Date: Sun, 11 Sep 2011 16:33:54 -0400 > From: jalem...@vt.edu > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] analysis of PMF calculations > > > > Rebeca García Fandiño wrote: > > Hi, > > thanks a lot for your quick answer... > > However, when I try the options you suggest for -cycl/nocycl, the > > program indeed ask for arguments: > > > > --- > > Program g_wham, VERSION 4.5 > > Source code file: statutil.c, line: 338 > > > > Fatal error: > > Expected a string argument for option -cycl > > - > > > > Upgrade to version 4.5.4 and try again. There have been improvements to > g_wham. > > > Besides, I think you have misunderstood me. When I use the option -cycl > > YES it's when I obtain the second column with zeros. I am working with a > > Based on what your message said, I thought I understood perfectly. Quoting: > > --- > When I use: > > /GROMACS/4.5/32/bin/g_wham -bins 100 -temp 300 -tol 0.0001 -min -2.4750 -max > 2.4750 -o pmf_1_cycl.xvg -hist histogram_cycl.xvg -ip ./pdo-files.dat -cycl > yes > > I get a curve with no errors, however if I don't use the option "-cycl yes" > --- > > Here everything sounds like it worked as expected and then you report the > error, > quoting again: > > --- > /GROMACS/4.5/32/bin/g_wham -bins 100 -temp 300 -tol 0.0001 -min -2.4750 -max > 2.4750 -o pmf_1_no_cycl.xvg -hist histogram_no_cycl.xvg -ip ./pdo-files.dat > > I get a profile where the second column is all "zero" > --- > > Nevertheless, you should still use version 4.5.4 g_wham and report back if > you > have problems. > > -Justin > > -- > > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] analysis of PMF calculations
Hi, thanks a lot for your quick answer... However, when I try the options you suggest for -cycl/nocycl, the program indeed ask for arguments: --- Program g_wham, VERSION 4.5 Source code file: statutil.c, line: 338 Fatal error: Expected a string argument for option -cycl - Besides, I think you have misunderstood me. When I use the option -cycl YES it's when I obtain the second column with zeros. I am working with a channel inserted into a membrane, but it is not exactly symmetric, this is why I would like to see the results obtained not using the option -cycl yes in Gromacs. Any suggestion? Thanks again for your help. Best wishes, Rebeca. > Date: Sun, 11 Sep 2011 15:55:34 -0400 > From: jalem...@vt.edu > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] analysis of PMF calculations > > > > Justin A. Lemkul wrote: > > > > > > Rebeca García Fandiño wrote: > >> Hello, > >> I have some old calculations (Umbrella Sampling) carried with Gromacs > >> 3.3.3 and I would like to analyze them using Gromacs 4. > >> When I use: > >> > >> /GROMACS/4.5/32/bin/g_wham -bins 100 -temp 300 -tol 0.0001 -min > >> -2.4750 -max 2.4750 -o pmf_1_cycl.xvg -hist histogram_cycl.xvg -ip > >> ./pdo-files.dat -cycl yes > >> > >> I get a curve with no errors, however if I don't use the option "-cycl > >> yes" > >> > > > > FYI, this syntax is wrong. Boolean options are -cycl/-nocycl. They do > > not take arguments. > > > >> /GROMACS/4.5/32/bin/g_wham -bins 100 -temp 300 -tol 0.0001 -min > >> -2.4750 -max 2.4750 -o pmf_1_no_cycl.xvg -hist histogram_no_cycl.xvg > >> -ip ./pdo-files.dat > >> > >> I get a profile where the second column is all "zero" > >> > > > > That makes sense. You're telling g_wham that you have a PMF starting > > and ending at the same place, but it's not a periodic profile. It can't > > debias the sampling windows over zero space. > > > >> The last lines of the analysis are (just in case it helps...): > >> (...) > >> 54700) Maximum change 1.204571e-02 > >> 54800) Maximum change 1.318242e-02 > >> 54900) Maximum change 1.235132e-02 > >> 55000) Maximum change 1.802996e-02 > >> 55100) Maximum change 1.166826e+00 > >> 55200) Maximum change inf > >> 55300) Maximum change 3.161195e-01 > >> 55400) Maximum change 3.437561e-01 > >> 55500) Maximum change inf > >> Switched to exact iteration in iteration 55501 > >> Converged in 55508 iterations. Final maximum change 0 > >> > >> I have tried to change to use the option "auto" to determine min and > >> max automatically, I have also tried to remove the tolerance (and set > >> the default), but the result was the same, I always obtain zero in the > >> second column without the option -cycl yes. > > > > Again, this would be incorrect syntax. The option "-cycl auto" does not > > exist. > > > > Sorry, read that wrong. The -auto option certainly exists, but the point > still > stands regarding the use of -cycl and its purpose. > > -Justin > > -- > > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] analysis of PMF calculations
Hello, I have some old calculations (Umbrella Sampling) carried with Gromacs 3.3.3 and I would like to analyze them using Gromacs 4. When I use: /GROMACS/4.5/32/bin/g_wham -bins 100 -temp 300 -tol 0.0001 -min -2.4750 -max 2.4750 -o pmf_1_cycl.xvg -hist histogram_cycl.xvg -ip ./pdo-files.dat -cycl yes I get a curve with no errors, however if I don't use the option "-cycl yes" /GROMACS/4.5/32/bin/g_wham -bins 100 -temp 300 -tol 0.0001 -min -2.4750 -max 2.4750 -o pmf_1_no_cycl.xvg -hist histogram_no_cycl.xvg -ip ./pdo-files.dat I get a profile where the second column is all "zero" The last lines of the analysis are (just in case it helps...): (...) 54700) Maximum change 1.204571e-02 54800) Maximum change 1.318242e-02 54900) Maximum change 1.235132e-02 55000) Maximum change 1.802996e-02 55100) Maximum change 1.166826e+00 55200) Maximum change inf 55300) Maximum change 3.161195e-01 55400) Maximum change 3.437561e-01 55500) Maximum change inf Switched to exact iteration in iteration 55501 Converged in 55508 iterations. Final maximum change 0 I have tried to change to use the option "auto" to determine min and max automatically, I have also tried to remove the tolerance (and set the default), but the result was the same, I always obtain zero in the second column without the option -cycl yes. Does anybody have any idea of what is happening? Why the second column in the PMF profile is set to zero? Thanks a lot for your help in advance. Dr. Rebeca Garcia Postdoctoral student Santiago de Compostela University Spain rega...@hotmail.com -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] append files in Gromacs 3.3
Thanks a lot for your quick answer! Best wishes, Rebeca. > Date: Wed, 10 Aug 2011 14:34:42 -0400 > From: jalem...@vt.edu > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] append files in Gromacs 3.3 > > > > Rebeca García Fandiño wrote: > > Hello, > > I have some old calculations (Umbrella Sampling) carried with Gromacs > > 3.3.3 and I need to extend them. > > I have tried to use the option "append" like in Gromacs 4.0, using: > > > > mdrun -v -np 8 -s Cl-2.4750_b.tpr -pi Cl-2.4750.ppa -po pullout.ppa -pn > > Cl-2.4750.ndx -pd -deffnm Cl-2.4750 -append > > > > but it does not work, the output files are not appended to the first ones. > > > > Right, because the -append option was added in version 4.0. > > > Do you know how could append files in Gromacs 3.3? > > > > Text files can be appended with standard Unix utilities like 'cat' while > other > Gromacs output files can be appended with other Gromacs utilities (trjcat for > trajectories, eneconv for energy files). > > -Justin > > > Thanks a lot for your help in advance. > > > > Best wishes, > > > > Rebeca. > > > > Dr.Rebeca Garcia > > Postdoctoral student > > Santiago de Compostela University > > Spain > > > > -- > > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] append files in Gromacs 3.3
Hello, I have some old calculations (Umbrella Sampling) carried with Gromacs 3.3.3 and I need to extend them. I have tried to use the option "append" like in Gromacs 4.0, using: mdrun -v -np 8 -s Cl-2.4750_b.tpr -pi Cl-2.4750.ppa -po pullout.ppa -pn Cl-2.4750.ndx -pd -deffnm Cl-2.4750 -append but it does not work, the output files are not appended to the first ones. Do you know how could append files in Gromacs 3.3? Thanks a lot for your help in advance. Best wishes, Rebeca. Dr.Rebeca Garcia Postdoctoral student Santiago de Compostela University Spain -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] large error bars in PMF
Hello, some days ago you had recomended me to use a dodecahedron box and "pull_dim = Y Y Y" to try to decrease some error bars I was obtaining in my PMF calculations (trying to calculate the binding energy of two cyclic peptides). Now, I have run these calaculations, but I have a doubt for the analysis. How should I analyze the results, using g_wham like in the case of "pull_dim = N N Y". I have not seen any option in g_wham to indicate this is a 3D PMF. I have also seen in this list these days that 3D-Wham was recomended (for a case different to mine). So, how should analyze the results obtaind from "pull_dim = Y Y Y" ? Thanks a lot for your help. Best wishes, Rebeca. From: rega...@hotmail.com To: gmx-users@gromacs.org Subject: RE: [gmx-users] large error bars in PMF Date: Fri, 22 Jul 2011 12:41:34 + I have used a cubic box of dimensions 8 x 8 x 14 (nm), and my total pulling was 5nm along the z direction. I dont´t think there could be a problem with the PBC, since the layer of solvent around the protein is quite big, although I suppose that using a dodecahedron box for this system would have been better. I will try now the "pull_dim = Y Y Y" and see what it happens. Thanks a lot for the suggestions! Best wishes, Rebeca. > Date: Fri, 22 Jul 2011 08:23:18 -0400 > From: chris.ne...@utoronto.ca > To: gmx-users@gromacs.org > Subject: [gmx-users] large error bars in PMF > > I see now what you mean. As it happens, I doubt that this would have > caused the problem since no force was applied on X and Y dimensions, > so it would require that there was a PBC-based distance degeneracy > along Z, although this is of course possible and hopefully Rebecca > will answer this part. > > Also, thanks for the pull_dimension/pull_vec fix. > > Chris. > > -- original message -- > > > chris.ne...@utoronto.ca wrote: > > [Hide Quoted Text] > I don't see why the box-type makes any difference whatsoever. It is > possible that if you use a rhombic dodecahedron, you may reduce the > system size, thus simulate more ns/day, thus converge faster, but that > should be the only effect. I would be interested to hear more from > Justin about how the box-shape is expected to affect peptide rotation... > perhaps I misunderstand this point. > My point was not that the box shape has any effect on protein rotation. That > will happen regardless of the box shape, of course. My suggestion for > this box > type was that since Rebeca has a system that is essentially spherically > symmetric (i.e. two proteins connected by some arbitrary vector, which are at > the same time rotating freely), then she must use a suitable box shape that > reflects this type of symmetry. I never got a clear answer to whether or not > the weird interactions she cited were due to PBC or not, but if one uses a > rectangular box for a system like this one, there can be artificial > interactions > very easily. > > [Hide Quoted Text] > I have a few other comments. > > 1. If you allow the peptide to rotate freely, then you do indeed need to > converge all of their different rotational interactions. An alternative > is to apply orientational restraints during the pulling (assuming that > you know the bound state) and then to correct to an unrestrained state > at large separations. You can see, for instance, D. L. Mobley, J. D. > Chodera, K. A. Dill. "On the use of orientational restraints and > symmetry number corrections in alchemical free energy calculations", ... > > 2. You are using "pull_dim = N N Y" which, if I haven't entirely > forgotten how the pull-code works, means that the distance along Z is > restrained but the distance along X and Y is free to change. What you > end up with by sampling in this way is pretty strange and will require a > really weird volumetric correction in the absence of infinite sampling > time. You must decide to either: (i) pull to a spherical distance: > > pull_dim = Y Y Y > pull_geometry = distance > > or (ii) to pull along a defined vector > > pull_dim = Y Y Y > pull_geometry = direction > Just a note here - if you set direction geometry, the pull_dim keyword is not > used, but pull_vec is. > > -Justin > > [Hide Quoted Text] > What you have done: > > pull_dim = N N Y > pull_geometry = distance > > is only really useful when the system is isotropic along the XY plane > (at least in the time averaged sense), such as for a lipid bilayer, or > when the freedom in X and Y is very low, such as in a channel. > > 3. Finally, just because you sampled *more* doesn't mean that your > values are converged. Look into block averaging and test to see if your > binding free energy is drifting over time. > > Good luck, > Chris. > > -- original message -- > > Hi again, > I have one doub about the suggestion of using a dodecahedral box for my > umbrella sampling to remove the problems I am having with the peptides > rotating. I cannot see why a dodecaheral box is going to avoid this. > Would it be be
RE: [gmx-users] large error bars in PMF
I have used a cubic box of dimensions 8 x 8 x 14 (nm), and my total pulling was 5nm along the z direction. I dont´t think there could be a problem with the PBC, since the layer of solvent around the protein is quite big, although I suppose that using a dodecahedron box for this system would have been better. I will try now the "pull_dim = Y Y Y" and see what it happens. Thanks a lot for the suggestions! Best wishes, Rebeca. > Date: Fri, 22 Jul 2011 08:23:18 -0400 > From: chris.ne...@utoronto.ca > To: gmx-users@gromacs.org > Subject: [gmx-users] large error bars in PMF > > I see now what you mean. As it happens, I doubt that this would have > caused the problem since no force was applied on X and Y dimensions, > so it would require that there was a PBC-based distance degeneracy > along Z, although this is of course possible and hopefully Rebecca > will answer this part. > > Also, thanks for the pull_dimension/pull_vec fix. > > Chris. > > -- original message -- > > > chris.ne...@utoronto.ca wrote: > > [Hide Quoted Text] > I don't see why the box-type makes any difference whatsoever. It is > possible that if you use a rhombic dodecahedron, you may reduce the > system size, thus simulate more ns/day, thus converge faster, but that > should be the only effect. I would be interested to hear more from > Justin about how the box-shape is expected to affect peptide rotation... > perhaps I misunderstand this point. > My point was not that the box shape has any effect on protein rotation. That > will happen regardless of the box shape, of course. My suggestion for > this box > type was that since Rebeca has a system that is essentially spherically > symmetric (i.e. two proteins connected by some arbitrary vector, which are at > the same time rotating freely), then she must use a suitable box shape that > reflects this type of symmetry. I never got a clear answer to whether or not > the weird interactions she cited were due to PBC or not, but if one uses a > rectangular box for a system like this one, there can be artificial > interactions > very easily. > > [Hide Quoted Text] > I have a few other comments. > > 1. If you allow the peptide to rotate freely, then you do indeed need to > converge all of their different rotational interactions. An alternative > is to apply orientational restraints during the pulling (assuming that > you know the bound state) and then to correct to an unrestrained state > at large separations. You can see, for instance, D. L. Mobley, J. D. > Chodera, K. A. Dill. "On the use of orientational restraints and > symmetry number corrections in alchemical free energy calculations", ... > > 2. You are using "pull_dim = N N Y" which, if I haven't entirely > forgotten how the pull-code works, means that the distance along Z is > restrained but the distance along X and Y is free to change. What you > end up with by sampling in this way is pretty strange and will require a > really weird volumetric correction in the absence of infinite sampling > time. You must decide to either: (i) pull to a spherical distance: > > pull_dim = Y Y Y > pull_geometry = distance > > or (ii) to pull along a defined vector > > pull_dim = Y Y Y > pull_geometry = direction > Just a note here - if you set direction geometry, the pull_dim keyword is not > used, but pull_vec is. > > -Justin > > [Hide Quoted Text] > What you have done: > > pull_dim = N N Y > pull_geometry = distance > > is only really useful when the system is isotropic along the XY plane > (at least in the time averaged sense), such as for a lipid bilayer, or > when the freedom in X and Y is very low, such as in a channel. > > 3. Finally, just because you sampled *more* doesn't mean that your > values are converged. Look into block averaging and test to see if your > binding free energy is drifting over time. > > Good luck, > Chris. > > -- original message -- > > Hi again, > I have one doub about the suggestion of using a dodecahedral box for my > umbrella sampling to remove the problems I am having with the peptides > rotating. I cannot see why a dodecaheral box is going to avoid this. > Would it be better a truncated octahedron? > Thanks a lot for your help. > Best wishes, > Rebeca. > > <... snip...> > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface
RE: [gmx-users] large error bars in PMF
Forget my last mail, I was not seeing the box correctly. Sorry about that. Best wishes, Rebeca. From: rega...@hotmail.com To: jalem...@vt.edu; gmx-users@gromacs.org Subject: RE: [gmx-users] large error bars in PMF Date: Fri, 22 Jul 2011 10:15:27 + CC: Hi again, I have one doub about the suggestion of using a dodecahedral box for my umbrella sampling to remove the problems I am having with the peptides rotating. I cannot see why a dodecaheral box is going to avoid this. Would it be better a truncated octahedron? Thanks a lot for your help. Best wishes, Rebeca. > Date: Thu, 21 Jul 2011 15:16:52 -0400 > From: jalem...@vt.edu > To: gmx-users@gromacs.org > Subject: Re: FW: [gmx-users] large error bars in PMF > > > > Rebeca García Fandiño wrote: > > > > > > I am trying to achieve the binding energy of the dimer composed by the > > two small cyclic peptides, to compare it with experimental. What > > advantages would I have using 3D PMF instead only 1D for this calculation? > > Intuitively, two molecules diffuse through solution until they find one > another, > which to me sounds a lot like a 3D path. Further, using a dodecahedral box > for > your umbrella sampling removes the problems you're having with the peptides > rotating. It sounds like you're trying to pull in one direction along a > rectangular box, but the peptides are not playing nice. I feel like this > discussion has come up at least once or twice before, though... > > -Justin > > > Thanks a lot! > > Rebeca. > > > > > Date: Thu, 21 Jul 2011 14:14:44 -0400 > > > From: jalem...@vt.edu > > > To: gmx-users@gromacs.org > > > Subject: Re: [gmx-users] large error bars in PMF > > > > > > > > > > > > Rebeca García Fandiño wrote: > > > > Hi, > > > > thanks a lot for your quick answer. > > > > What I am trying to pull are two small peptides one from another (r_1 > > > > and r_2). > > > > I did not understand very well your last suggestion: "...if you want > > > > reasonable error bars you will not lots of well-converged data". > > > > > > Oops, that should have read "you will *need* lots of well-converged > > data." > > > > > > > Do you mean I will need also more windows besides extending the > > simulations? > > > > > > I doubt you need more windows. Likely you just need more time in each. > > > > > > > I think the problem could be also that the peptides I am using > > rotate in > > > > the box and they do not remain flat one respect to the other. They > > > > gyrate freely and some parts of their structure interact along the > > > > pulling... > > > > > > Interactions are part of the dissociation process and are not > > problematic per > > > se. But if you're trying to obtain only a one-dimensional PMF then your > > > rotation could be a problem. Is there some reason you need a > > one-dimensional > > > PMF and not a three-dimensional PMF? What are you trying to achieve? > > > > > > -Justin > > > > > > > Thanks a lot again for your help. > > > > Best wishes, > > > > Rebeca. > > > > > > > > > > > > > > > > > > > > > > From: rega...@hotmail.com > > > > To: gmx-users@gromacs.org > > > > Date: Thu, 21 Jul 2011 16:36:59 + > > > > Subject: [gmx-users] large error bars in PMF > > > > > > > > > > > > Hi, > > > > I am trying to calculate the binding energy of two molecules using the > > > > PMF (Umbrella Sampling method) and Gromacs 4.0. > > > > Some weeks ago I have written to the list because changing the > > number of > > > > windows used in the Umbrella Sampling calculations different results > > > > were obtained, and I was suggested to extend my simulations since the > > > > error bars associated to each windows were too high. > > > > I have now extended my simulations from 1 ns to 8 ns, however, I > > cannot > > > > see much different from the shorter calculations. I send you the > > > > comparison of the two PMF including the error bars (attached). > > > > Now I am using 50 windows, but the shorter simulations were done using > > > > 100 windows, so I don'
RE: [gmx-users] large error bars in PMF
Hi again, I have one doub about the suggestion of using a dodecahedral box for my umbrella sampling to remove the problems I am having with the peptides rotating. I cannot see why a dodecaheral box is going to avoid this. Would it be better a truncated octahedron? Thanks a lot for your help. Best wishes, Rebeca. > Date: Thu, 21 Jul 2011 15:16:52 -0400 > From: jalem...@vt.edu > To: gmx-users@gromacs.org > Subject: Re: FW: [gmx-users] large error bars in PMF > > > > Rebeca García Fandiño wrote: > > > > > > I am trying to achieve the binding energy of the dimer composed by the > > two small cyclic peptides, to compare it with experimental. What > > advantages would I have using 3D PMF instead only 1D for this calculation? > > Intuitively, two molecules diffuse through solution until they find one > another, > which to me sounds a lot like a 3D path. Further, using a dodecahedral box > for > your umbrella sampling removes the problems you're having with the peptides > rotating. It sounds like you're trying to pull in one direction along a > rectangular box, but the peptides are not playing nice. I feel like this > discussion has come up at least once or twice before, though... > > -Justin > > > Thanks a lot! > > Rebeca. > > > > > Date: Thu, 21 Jul 2011 14:14:44 -0400 > > > From: jalem...@vt.edu > > > To: gmx-users@gromacs.org > > > Subject: Re: [gmx-users] large error bars in PMF > > > > > > > > > > > > Rebeca García Fandiño wrote: > > > > Hi, > > > > thanks a lot for your quick answer. > > > > What I am trying to pull are two small peptides one from another (r_1 > > > > and r_2). > > > > I did not understand very well your last suggestion: "...if you want > > > > reasonable error bars you will not lots of well-converged data". > > > > > > Oops, that should have read "you will *need* lots of well-converged > > data." > > > > > > > Do you mean I will need also more windows besides extending the > > simulations? > > > > > > I doubt you need more windows. Likely you just need more time in each. > > > > > > > I think the problem could be also that the peptides I am using > > rotate in > > > > the box and they do not remain flat one respect to the other. They > > > > gyrate freely and some parts of their structure interact along the > > > > pulling... > > > > > > Interactions are part of the dissociation process and are not > > problematic per > > > se. But if you're trying to obtain only a one-dimensional PMF then your > > > rotation could be a problem. Is there some reason you need a > > one-dimensional > > > PMF and not a three-dimensional PMF? What are you trying to achieve? > > > > > > -Justin > > > > > > > Thanks a lot again for your help. > > > > Best wishes, > > > > Rebeca. > > > > > > > > > > > > > > > > > > > > > > From: rega...@hotmail.com > > > > To: gmx-users@gromacs.org > > > > Date: Thu, 21 Jul 2011 16:36:59 + > > > > Subject: [gmx-users] large error bars in PMF > > > > > > > > > > > > Hi, > > > > I am trying to calculate the binding energy of two molecules using the > > > > PMF (Umbrella Sampling method) and Gromacs 4.0. > > > > Some weeks ago I have written to the list because changing the > > number of > > > > windows used in the Umbrella Sampling calculations different results > > > > were obtained, and I was suggested to extend my simulations since the > > > > error bars associated to each windows were too high. > > > > I have now extended my simulations from 1 ns to 8 ns, however, I > > cannot > > > > see much different from the shorter calculations. I send you the > > > > comparison of the two PMF including the error bars (attached). > > > > Now I am using 50 windows, but the shorter simulations were done using > > > > 100 windows, so I don't think increasing the number of windows > > could help. > > > > My system has about 29200 atoms (where 29000 are chloroform atoms). > > The > > > > *mdp file I am using is copied below. > > > > Would you have any suggestio
RE: [gmx-users] large error bars in PMF
Thanks for your answer.
My peptide has 6 residues and it is cyclic.
I calculated the errors through bootstrap, using this:
g_wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kCal -b 500 -n
Bootstrap 200
Are the pmfs aligned on the minimum distance value? Is that the value by
default? How could I calculate the errors based on the PMFs aligned on the long
distance value?
Thanks a lot for all the help.
Best wishes,
Rebeca.
> From: x.peri...@rug.nl
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] large error bars in PMF
> Date: Thu, 21 Jul 2011 14:33:28 -0600
>
>
> One potential problem you have is that as Justin mentioned your minimum
> is not well defined and certain much less well sampled than the long
> distances
> windows. Small peptides (depends the size) may sample relevant phase
> space to get reasonable convergence within 8 ns when free in solution;
> in contact certainly not ...
>
> How long is you peptide?
>
> You might get a better estimate of your error by plotting all the pmfs
> you've
> got through bootstrap (if this is the case) ... and get the errors
> based on the
> pmfs aligned on the long distance value and not on the "minimum" which
> is
> probably what you did ... if the minimum is not well defined then it
> does not
> make sense.
>
> On Jul 21, 2011, at 1:36 PM, Justin A. Lemkul wrote:
>
> >
> >
> > Rebeca García Fandiño wrote:
> >> OK,
> >> I will try a dodecahedral box and also to extend my actual
> >> simulations.
> >> Could you give me some advice about starting to learn about 3D PMF?
> >> I have not seen this in the manual, and I have never used it
> >> before. I have only found your tutorial about how to calculate PMF
> >> in Gromacs 4...
> >
> > In practice, there's basically nothing different between 3D and 1D.
> > You specify the dimensions to which the biasing potential is applied
> > with pull_dim or pull_vec (depending on the pull_geometry used).
> > Right now you're calculating the PMF along the z-dimension only
> > ("pull_dim = N N Y"), which may be appropriate for one-dimensional
> > processes or those in which the reference group does not rotate much
> > in the timeframe of the sampling. Setting "pull_dim = Y Y Y" will
> > apply the restraint in all dimensions.
> >
> > -Justin
> >
> >> Thanks a lot again for your help.
> >> Best wishes,
> >> Rebeca.
> >> > Date: Thu, 21 Jul 2011 15:16:52 -0400
> >> > From: jalem...@vt.edu
> >> > To: gmx-users@gromacs.org
> >> > Subject: Re: FW: [gmx-users] large error bars in PMF
> >> >
> >> >
> >> >
> >> > Rebeca García Fandiño wrote:
> >> > >
> >> > >
> >> > > I am trying to achieve the binding energy of the dimer composed
> >> by the
> >> > > two small cyclic peptides, to compare it with experimental. What
> >> > > advantages would I have using 3D PMF instead only 1D for this
> >> calculation?
> >> >
> >> > Intuitively, two molecules diffuse through solution until they
> >> find one another,
> >> > which to me sounds a lot like a 3D path. Further, using a
> >> dodecahedral box for
> >> > your umbrella sampling removes the problems you're having with
> >> the peptides
> >> > rotating. It sounds like you're trying to pull in one direction
> >> along a
> >> > rectangular box, but the peptides are not playing nice. I feel
> >> like this
> >> > discussion has come up at least once or twice before, though...
> >> >
> >> > -Justin
> >> >
> >> > > Thanks a lot!
> >> > > Rebeca.
> >> > >
> >> > > > Date: Thu, 21 Jul 2011 14:14:44 -0400
> >> > > > From: jalem...@vt.edu
> >> > > > To: gmx-users@gromacs.org
> >> > > > Subject: Re: [gmx-users] large error bars in PMF
> >> > > >
> >> > > >
> >> > > >
> >> > > > Rebeca García Fandiño wrote:
> >> > > > > Hi,
> >> > > > > thanks a lot for your quick answer.
> >> > > > > What I am trying to pull are two small peptides one from
> >> another (r_1
> >> > > > > and r_2).
> >> > > > > I did not understand very well your last suggestion: "...if
> >> you wan
RE: [gmx-users] large error bars in PMF
OK, I will try a dodecahedral box and also to extend my actual simulations. Could you give me some advice about starting to learn about 3D PMF? I have not seen this in the manual, and I have never used it before. I have only found your tutorial about how to calculate PMF in Gromacs 4... Thanks a lot again for your help. Best wishes, Rebeca. > Date: Thu, 21 Jul 2011 15:16:52 -0400 > From: jalem...@vt.edu > To: gmx-users@gromacs.org > Subject: Re: FW: [gmx-users] large error bars in PMF > > > > Rebeca García Fandiño wrote: > > > > > > I am trying to achieve the binding energy of the dimer composed by the > > two small cyclic peptides, to compare it with experimental. What > > advantages would I have using 3D PMF instead only 1D for this calculation? > > Intuitively, two molecules diffuse through solution until they find one > another, > which to me sounds a lot like a 3D path. Further, using a dodecahedral box > for > your umbrella sampling removes the problems you're having with the peptides > rotating. It sounds like you're trying to pull in one direction along a > rectangular box, but the peptides are not playing nice. I feel like this > discussion has come up at least once or twice before, though... > > -Justin > > > Thanks a lot! > > Rebeca. > > > > > Date: Thu, 21 Jul 2011 14:14:44 -0400 > > > From: jalem...@vt.edu > > > To: gmx-users@gromacs.org > > > Subject: Re: [gmx-users] large error bars in PMF > > > > > > > > > > > > Rebeca García Fandiño wrote: > > > > Hi, > > > > thanks a lot for your quick answer. > > > > What I am trying to pull are two small peptides one from another (r_1 > > > > and r_2). > > > > I did not understand very well your last suggestion: "...if you want > > > > reasonable error bars you will not lots of well-converged data". > > > > > > Oops, that should have read "you will *need* lots of well-converged > > data." > > > > > > > Do you mean I will need also more windows besides extending the > > simulations? > > > > > > I doubt you need more windows. Likely you just need more time in each. > > > > > > > I think the problem could be also that the peptides I am using > > rotate in > > > > the box and they do not remain flat one respect to the other. They > > > > gyrate freely and some parts of their structure interact along the > > > > pulling... > > > > > > Interactions are part of the dissociation process and are not > > problematic per > > > se. But if you're trying to obtain only a one-dimensional PMF then your > > > rotation could be a problem. Is there some reason you need a > > one-dimensional > > > PMF and not a three-dimensional PMF? What are you trying to achieve? > > > > > > -Justin > > > > > > > Thanks a lot again for your help. > > > > Best wishes, > > > > Rebeca. > > > > > > > > > > > > > > > > > > > > > > From: rega...@hotmail.com > > > > To: gmx-users@gromacs.org > > > > Date: Thu, 21 Jul 2011 16:36:59 + > > > > Subject: [gmx-users] large error bars in PMF > > > > > > > > > > > > Hi, > > > > I am trying to calculate the binding energy of two molecules using the > > > > PMF (Umbrella Sampling method) and Gromacs 4.0. > > > > Some weeks ago I have written to the list because changing the > > number of > > > > windows used in the Umbrella Sampling calculations different results > > > > were obtained, and I was suggested to extend my simulations since the > > > > error bars associated to each windows were too high. > > > > I have now extended my simulations from 1 ns to 8 ns, however, I > > cannot > > > > see much different from the shorter calculations. I send you the > > > > comparison of the two PMF including the error bars (attached). > > > > Now I am using 50 windows, but the shorter simulations were done using > > > > 100 windows, so I don't think increasing the number of windows > > could help. > > > > My system has about 29200 atoms (where 29000 are chloroform atoms). > > The > > > > *mdp file I am using is copied below. > > > >
FW: [gmx-users] large error bars in PMF
I am trying to achieve the binding energy of the dimer composed by the two small cyclic peptides, to compare it with experimental. What advantages would I have using 3D PMF instead only 1D for this calculation? Thanks a lot! Rebeca. > Date: Thu, 21 Jul 2011 14:14:44 -0400 > From: jalem...@vt.edu > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] large error bars in PMF > > > > Rebeca García Fandiño wrote: > > Hi, > > thanks a lot for your quick answer. > > What I am trying to pull are two small peptides one from another (r_1 > > and r_2). > > I did not understand very well your last suggestion: "...if you want > > reasonable error bars you will not lots of well-converged data". > > Oops, that should have read "you will *need* lots of well-converged data." > > > Do you mean I will need also more windows besides extending the simulations? > > I doubt you need more windows. Likely you just need more time in each. > > > I think the problem could be also that the peptides I am using rotate in > > the box and they do not remain flat one respect to the other. They > > gyrate freely and some parts of their structure interact along the > > pulling... > > Interactions are part of the dissociation process and are not problematic per > se. But if you're trying to obtain only a one-dimensional PMF then your > rotation could be a problem. Is there some reason you need a one-dimensional > PMF and not a three-dimensional PMF? What are you trying to achieve? > > -Justin > > > Thanks a lot again for your help. > > Best wishes, > > Rebeca. > > > > > > > > > > From: rega...@hotmail.com > > To: gmx-users@gromacs.org > > Date: Thu, 21 Jul 2011 16:36:59 + > > Subject: [gmx-users] large error bars in PMF > > > > > > Hi, > > I am trying to calculate the binding energy of two molecules using the > > PMF (Umbrella Sampling method) and Gromacs 4.0. > > Some weeks ago I have written to the list because changing the number of > > windows used in the Umbrella Sampling calculations different results > > were obtained, and I was suggested to extend my simulations since the > > error bars associated to each windows were too high. > > I have now extended my simulations from 1 ns to 8 ns, however, I cannot > > see much different from the shorter calculations. I send you the > > comparison of the two PMF including the error bars (attached). > > Now I am using 50 windows, but the shorter simulations were done using > > 100 windows, so I don't think increasing the number of windows could help. > > My system has about 29200 atoms (where 29000 are chloroform atoms). The > > *mdp file I am using is copied below. > > Would you have any suggestion to improve the results and decrease the > > error bars in the calculations? > > > > MDP file--- > > title = Umbrella pulling simulation > > define = > > define = > > ; Run parameters > > integrator = md > > dt = 0.002 > > tinit = 0 > > nsteps = 50 ; 1 ns > > nstcomm = 10 > > ; Output parameters > > nstxout = 5000 ; every 10 ps > > nstvout = 5000 > > nstfout = 5000 > > nstxtcout = 5000 ; every 10 ps > > nstenergy = 5000 > > ; Bond parameters > > constraint_algorithm= lincs > > constraints = all-bonds > > continuation= yes > > ; Single-range cutoff scheme > > nstlist = 5 > > ns_type = grid > > rlist = 1.4 > > rcoulomb= 1.4 > > rvdw= 1.4 > > ; PME electrostatics parameters > > coulombtype = PME > > fourierspacing = 0.12 > > fourier_nx = 0 > > fourier_ny = 0 > > fourier_nz = 0 > > pme_order = 4 > > ewald_rtol = 1e-5 > > optimize_fft= yes > > ; Berendsen temperature coupling is on in two groups > > Tcoupl = Nose-Hoover > > tc_grps = ACH CL3 > > tau_t = 0.5 0.5 > > ref_t = 300 300 > > ; Pressure coupling is on > > Pcoupl = Parrinello-Rahman > > pcoupltype = isotropic > > tau_p = 1.0 > > compressibility = 4.5e-5 > > ref_p = 1.0 > > ; Generate velocities is off > > gen_vel = no > > ; Periodic boundary conditions are on in all directions > > pbc = xyz > > ; Lo
RE: [gmx-users] large error bars in PMF
Hi, thanks a lot for your quick answer. What I am trying to pull are two small peptides one from another (r_1 and r_2). I did not understand very well your last suggestion: "...if you want reasonable error bars you will not lots of well-converged data". Do you mean I will need also more windows besides extending the simulations? I think the problem could be also that the peptides I am using rotate in the box and they do not remain flat one respect to the other. They gyrate freely and some parts of their structure interact along the pulling... Thanks a lot again for your help. Best wishes, Rebeca. From: rega...@hotmail.com To: gmx-users@gromacs.org Date: Thu, 21 Jul 2011 16:36:59 + Subject: [gmx-users] large error bars in PMF Hi, I am trying to calculate the binding energy of two molecules using the PMF (Umbrella Sampling method) and Gromacs 4.0. Some weeks ago I have written to the list because changing the number of windows used in the Umbrella Sampling calculations different results were obtained, and I was suggested to extend my simulations since the error bars associated to each windows were too high. I have now extended my simulations from 1 ns to 8 ns, however, I cannot see much different from the shorter calculations. I send you the comparison of the two PMF including the error bars (attached). Now I am using 50 windows, but the shorter simulations were done using 100 windows, so I don't think increasing the number of windows could help. My system has about 29200 atoms (where 29000 are chloroform atoms). The *mdp file I am using is copied below. Would you have any suggestion to improve the results and decrease the error bars in the calculations? MDP file--- title = Umbrella pulling simulation define = define = ; Run parameters integrator = md dt = 0.002 tinit = 0 nsteps = 50 ; 1 ns nstcomm = 10 ; Output parameters nstxout = 5000 ; every 10 ps nstvout = 5000 nstfout = 5000 nstxtcout = 5000 ; every 10 ps nstenergy = 5000 ; Bond parameters constraint_algorithm= lincs constraints = all-bonds continuation= yes ; Single-range cutoff scheme nstlist = 5 ns_type = grid rlist = 1.4 rcoulomb= 1.4 rvdw= 1.4 ; PME electrostatics parameters coulombtype = PME fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft= yes ; Berendsen temperature coupling is on in two groups Tcoupl = Nose-Hoover tc_grps = ACH CL3 tau_t = 0.5 0.5 ref_t = 300 300 ; Pressure coupling is on Pcoupl = Parrinello-Rahman pcoupltype = isotropic tau_p = 1.0 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocities is off gen_vel = no ; Periodic boundary conditions are on in all directions pbc = xyz ; Long-range dispersion correction DispCorr= EnerPres ; Pull code pull= umbrella pull_geometry = distance pull_dim= N N Y pull_start = yes pull_ngroups= 1 pull_group0 = r_1 pull_group1 = r_2 pull_init1 = 0 pull_rate1 = 0.0 pull_k1 = 1000 ; kJ mol^-1 nm^-2 pull_nstxout= 1000 ; every 2 ps pull_nstfout= 1000 ; every 2 ps --- Thanks a lot in advance. Best wishes, Dr. Rebeca Garcia Santiago de Compostela University Spain -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] large error bars in PMF
Hi, I am trying to calculate the binding energy of two molecules using the PMF (Umbrella Sampling method) and Gromacs 4.0. Some weeks ago I have written to the list because changing the number of windows used in the Umbrella Sampling calculations different results were obtained, and I was suggested to extend my simulations since the error bars associated to each windows were too high. I have now extended my simulations from 1 ns to 8 ns, however, I cannot see much different from the shorter calculations. I send you the comparison of the two PMF including the error bars (attached). Now I am using 50 windows, but the shorter simulations were done using 100 windows, so I don't think increasing the number of windows could help. My system has about 29200 atoms (where 29000 are chloroform atoms). The *mdp file I am using is copied below. Would you have any suggestion to improve the results and decrease the error bars in the calculations? MDP file--- title = Umbrella pulling simulation define = define = ; Run parameters integrator = md dt = 0.002 tinit = 0 nsteps = 50 ; 1 ns nstcomm = 10 ; Output parameters nstxout = 5000 ; every 10 ps nstvout = 5000 nstfout = 5000 nstxtcout = 5000 ; every 10 ps nstenergy = 5000 ; Bond parameters constraint_algorithm= lincs constraints = all-bonds continuation= yes ; Single-range cutoff scheme nstlist = 5 ns_type = grid rlist = 1.4 rcoulomb= 1.4 rvdw= 1.4 ; PME electrostatics parameters coulombtype = PME fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft= yes ; Berendsen temperature coupling is on in two groups Tcoupl = Nose-Hoover tc_grps = ACH CL3 tau_t = 0.5 0.5 ref_t = 300 300 ; Pressure coupling is on Pcoupl = Parrinello-Rahman pcoupltype = isotropic tau_p = 1.0 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocities is off gen_vel = no ; Periodic boundary conditions are on in all directions pbc = xyz ; Long-range dispersion correction DispCorr= EnerPres ; Pull code pull= umbrella pull_geometry = distance pull_dim= N N Y pull_start = yes pull_ngroups= 1 pull_group0 = r_1 pull_group1 = r_2 pull_init1 = 0 pull_rate1 = 0.0 pull_k1 = 1000 ; kJ mol^-1 nm^-2 pull_nstxout= 1000 ; every 2 ps pull_nstfout= 1000 ; every 2 ps --- Thanks a lot in advance. Best wishes, Dr. Rebeca Garcia Santiago de Compostela University Spain comparation_shorter_longer_PMF.pdf Description: Adobe PDF document -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] extending PMF
Hello, I am trying to extend a PMF calculation (Umbrella Sampling calculation). In first place I used tpbconv: tpbconv -s umbrella_3.tpr -o umbrella_3b.tpr -extend 1000 And then I run it using mdrun: mdrun -s umbrella_3b.tpr -cpi umbrella_3.cpt -pf pullf-umbrella_3.xvg -px pullx-umbrella_3.xvg -append I got the following error: . (...) Reading file umbrella_3b.tpr, VERSION 4.0.7 (single precision) Reading checkpoint file umbrella_3.cpt generated: Fri Jul 1 00:18:26 2011tpbconv -s umbrella_3.tpr -o umbrella_3b.tpr -extend 1000 --- Program mdrun, VERSION 4.0.7 Source code file: checkpoint.c, line: 1261 Fatal error: Truncation of file umbrella_3.trr failed. --- "set: No match." (tcsh) Error on node 0, will try to stop all the nodes Halting parallel program mdrun on CPU 0 out of 8 gcq#269: "set: No match." (tcsh) ... Do I need the *trr files for extending the simulation. In a normal calculation, the *cpt is enough for extending a simulation. Is any difference for the PMF calculations? Thanks a lot in advance. Best wishes, Dr. Rebeca Garcia Santiago de Compostela University Spain -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] number of windows in PMF
Thanks again for your quick answer! No, I did not prior equilibration, however for the analysis I was considering only the last 0.5 ns. I will try to extend the simulations and see what happens. Is it possible to do it using tpbconv as in a typical simulation? Should I create different files for pullf*.xvg and pullx*.xvg and then join them for the analysis? Best wishes, Rebeca. > Date: Tue, 12 Jul 2011 17:59:44 -0400 > From: jalem...@vt.edu > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] number of windows in PMF > > > > Justin A. Lemkul wrote: > > > > > > Rebeca García Fandiño wrote: > >> Thanks a lot for your answer. > >> My system have about 29000 atoms, and the simulation time was 1ns. > >> I have generated the error bars, and indeed you were right, they are > >> too big. The histograms looked good, so I thought they should be > >> well-converged...:S > >> What should I do, extending the simulation or generating more windows? > > > > The simulations probably need to be longer. I've gotten good > > convergence in much larger systems using far fewer windows but somewhat > > longer simulations. > > > > Another thing to consider (aside from my offhand guesses of simulation > length) > is that if you're generating velocities at the beginning of each simulation > in > each window in the absence of prior equilibration, you're not *really* > getting 1 > ns of viable data. Some should be discarded as equilibration, if you're not > doing that already. If you've done prior equilibration in each window, then > disregard this thought. > > -Justin > > -- > > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] number of windows in PMF
Thanks a lot for your answer. My system have about 29000 atoms, and the simulation time was 1ns. I have generated the error bars, and indeed you were right, they are too big. The histograms looked good, so I thought they should be well-converged...:S What should I do, extending the simulation or generating more windows? Thanks a lot again for your help. Best wishes, Rebeca. > Date: Tue, 12 Jul 2011 16:53:54 -0400 > From: jalem...@vt.edu > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] number of windows in PMF > > > > Rebeca García Fandiño wrote: > > Hello, > > I am trying to calculate the binding energy between two monomers in > > three different dimers, using PMF (Umbrella Sampling method) and > > following Justin's tutorial. > > Using 100 windows separated 0.05 nm I get the PMFs represented in > > "pmf_using_100_points.pdf" (attached), and using 50 windows separated > > 0.1 nm I get different PMF results, represented in "pmf_using_50_points.pdf" > > How is it possible to obtain so different results depending on the > > number of windows used in the Umbrella Sampling Calculation? > > You haven't said how long your simulations are or how large the system is. > It > looks to me like your curves are not well-converged. The energy minima are > not > at a consistent location along the reaction coordinate, so I suspect you're > not > yet converged. > > g_wham will give you an error estimate; you may find that you have large > error > bars, so the results may be indistinguishable (within error), but from the > plots > one cannot tell. > > -Justin > > > Any help is appreciated. > > Thanks a lot in advance! > > Best wishes, > > Rebeca. > > > > Dr. Rebeca Garcia > > Santiago de Compostela University > > Spain > > > > -- > > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] number of windows in PMF
Hello, I am trying to calculate the binding energy between two monomers in three different dimers, using PMF (Umbrella Sampling method) and following Justin's tutorial. Using 100 windows separated 0.05 nm I get the PMFs represented in "pmf_using_100_points.pdf" (attached), and using 50 windows separated 0.1 nm I get different PMF results, represented in "pmf_using_50_points.pdf" How is it possible to obtain so different results depending on the number of windows used in the Umbrella Sampling Calculation? Any help is appreciated. Thanks a lot in advance! Best wishes, Rebeca. Dr. Rebeca Garcia Santiago de Compostela University Spain pmf_using_100points.pdf Description: Adobe PDF document pmf_using_50points.pdf Description: Adobe PDF document -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] restraints in PMF (Justin's tutorial)
OK, I will try to increase the distances of the c.o.m of both molecules to eliminate any contact between them, adding more windows. Thanks a lot for your help! Best wishes, Rebeca. > Date: Wed, 22 Jun 2011 11:51:36 -0400 > From: jalem...@vt.edu > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] restraints in PMF (Justin's tutorial) > > > > Rebeca García Fandiño wrote: > > Thanks a lot for your quick answer! > > I think they are separated enough, however my monomers are cyclic (like > > discs); I start with a parallel conformation between then, but along the > > Umbrella simulation, both of them rotate and approach. > > If I do not use restraints, how could I avoid the rotation? > > > > You don't. Why wouldn't two molecules rotate freely in solution when binding > or > unbinding? It seems like completely natural behavior. Even in simple > systems > of protein-ligand association, part of the binding energy is the entropic > restriction of the ligand into a certain binding-competent pose. Why > wouldn't > that happen here? Sounds like an artificial notion to me. > > -Justin > > > I am using the following md_umbrella.mdp: > > > > title = Umbrella pulling simulation > > define = > > define = > > ; Run parameters > > integrator = md > > dt = 0.002 > > tinit = 0 > > nsteps = 50 ; 1 ns > > nstcomm = 10 > > ; Output parameters > > nstxout = 5000 > > nstvout = 5000 > > nstfout = 5000 > > nstxtcout = 5000 > > nstenergy = 5000 > > ; Bond parameters > > constraint_algorithm= lincs > > constraints = all-bonds > > continuation= yes > > ; Single-range cutoff scheme > > nstlist = 5 > > ns_type = grid > > rlist = 1.4 > > rcoulomb= 1.4 > > rvdw= 1.4 > > ; PME electrostatics parameters > > coulombtype = PME > > fourierspacing = 0.12 > > fourier_nx = 0 > > fourier_ny = 0 > > fourier_nz = 0 > > pme_order = 4 > > ewald_rtol = 1e-5 > > optimize_fft= yes > > ; Berendsen temperature coupling is on in two groups > > Tcoupl = Nose-Hoover > > tc_grps = r_1_r_2 CL3 > > tau_t = 0.5 0.5 > > ref_t = 300 300 > > ; Pressure coupling is on > > Pcoupl = Parrinello-Rahman > > pcoupltype = isotropic > > tau_p = 1.0 > > compressibility = 4.5e-5 > > ref_p = 1.0 > > ; Generate velocities is off > > gen_vel = no > > ; Periodic boundary conditions are on in all directions > > pbc = xyz > > ; Long-range dispersion correction > > DispCorr= EnerPres > > ; Pull code > > pull= umbrella > > pull_geometry = distance > > pull_dim= N N Y > > pull_start = yes > > pull_ngroups= 1 > > pull_group0 = r_1 > > pull_group1 = r_2 > > pull_init1 = 0 > > pull_rate1 = 0.0 > > pull_k1 = 1000 ; kJ mol^-1 nm^-2 > > pull_nstxout= 1000 ; every 2 ps > > pull_nstfout= 1000 ; every 2 ps > > > > Thanks a lot again for your help. > > > > Best wishes, > > > > Rebeca. > > > > > > > Date: Wed, 22 Jun 2011 10:53:16 -0400 > > > From: jalem...@vt.edu > > > To: gmx-users@gromacs.org > > > Subject: Re: [gmx-users] restraints in PMF (Justin's tutorial) > > > > > > > > > > > > Rebeca García Fandiño wrote: > > > > Hello, > > > > I am trying to obtain the PMF from Umbrella Sampling of the process of > > > > separating two monomers of a dimer, following Justin 's tutorial > > > > > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/index.html > > > > > > > > I have done the Umbrella Sampling simulations without using any > > > > restraints in any of the monomers, however, I can see that they > > move and > > > > gyrate so that although the c.o.m are separated from each other, there > > > > are parts of both interacting, in such way that they are not separated > > > > as they should be. > > > > > > > > Would it be correct if I apply restraints to both monomers in all the > > > > Umbrella Sampling simulations?. I have seen that in Justin's tutorial > > > > they applied restraints
RE: [gmx-users] restraints in PMF (Justin's tutorial)
Thanks a lot for your quick answer! I think they are separated enough, however my monomers are cyclic (like discs); I start with a parallel conformation between then, but along the Umbrella simulation, both of them rotate and approach. If I do not use restraints, how could I avoid the rotation? I am using the following md_umbrella.mdp: title = Umbrella pulling simulation define = define = ; Run parameters integrator = md dt = 0.002 tinit = 0 nsteps = 50 ; 1 ns nstcomm = 10 ; Output parameters nstxout = 5000 nstvout = 5000 nstfout = 5000 nstxtcout = 5000 nstenergy = 5000 ; Bond parameters constraint_algorithm= lincs constraints = all-bonds continuation= yes ; Single-range cutoff scheme nstlist = 5 ns_type = grid rlist = 1.4 rcoulomb= 1.4 rvdw= 1.4 ; PME electrostatics parameters coulombtype = PME fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft= yes ; Berendsen temperature coupling is on in two groups Tcoupl = Nose-Hoover tc_grps = r_1_r_2 CL3 tau_t = 0.5 0.5 ref_t = 300 300 ; Pressure coupling is on Pcoupl = Parrinello-Rahman pcoupltype = isotropic tau_p = 1.0 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocities is off gen_vel = no ; Periodic boundary conditions are on in all directions pbc = xyz ; Long-range dispersion correction DispCorr= EnerPres ; Pull code pull= umbrella pull_geometry = distance pull_dim= N N Y pull_start = yes pull_ngroups= 1 pull_group0 = r_1 pull_group1 = r_2 pull_init1 = 0 pull_rate1 = 0.0 pull_k1 = 1000 ; kJ mol^-1 nm^-2 pull_nstxout= 1000 ; every 2 ps pull_nstfout= 1000 ; every 2 ps Thanks a lot again for your help. Best wishes, Rebeca. > Date: Wed, 22 Jun 2011 10:53:16 -0400 > From: jalem...@vt.edu > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] restraints in PMF (Justin's tutorial) > > > > Rebeca García Fandiño wrote: > > Hello, > > I am trying to obtain the PMF from Umbrella Sampling of the process of > > separating two monomers of a dimer, following Justin 's tutorial > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/index.html > > > > I have done the Umbrella Sampling simulations without using any > > restraints in any of the monomers, however, I can see that they move and > > gyrate so that although the c.o.m are separated from each other, there > > are parts of both interacting, in such way that they are not separated > > as they should be. > > > > Would it be correct if I apply restraints to both monomers in all the > > Umbrella Sampling simulations?. I have seen that in Justin's tutorial > > they applied restraints to one of the chains, but in my case I think I > > will need to restrain both of the units. Would that be correct for the > > PMF calculation? > > > > There are no position restraints applied during the umbrella sampling > simulations. They are unnecessary. The umbrella potential is itself a > restraint to maintain COM separation. > > If parts of your proteins are interacting, you simply haven't fully separated > your monomers and you need to create configurations with greater COM > separation. > If you apply position restraints to fit some notion that your monomers > shouldn't interact at certain distances, then you're applying an unnatural > (and > potentially incorrect) bias, causing the PMF to converge incorrectly. > > -Justin > > > Thanks a lot in advance. > > > > Rebeca. > > > > > Date: Mon, 20 Jun 2011 17:03:56 -0400 > > > From: jalem...@vt.edu > > > To: rega...@hotmail.com > > > CC: gmx-users@gromacs.org > > > Subject: Re: doubt about your Umbrella Sampling tutorial > > > > > > > > > > > > Rebeca García Fandiño wrote: > > > > Dear Justin, > > > > my name is Rebeca and I am a postdoctoral student in Santiago de > > > > Compostela University. Sorry for disturbing you to your personal > > mail, I > > > > have tried to post to the Gromacs-list first, but I did not get any > > answer. > > > > > > I was traveling and not paying much attention to messages across the > > list. I > > > will CC this reply to the list in the hopes that it is useful to > > others, as well. > > > > > > > I am trying to obtain the PMF from Umbrella Sampling of the process of
[gmx-users] restraints in PMF (Justin's tutorial)
Hello, I am trying to obtain the PMF from Umbrella Sampling of the process of separating two monomers of a dimer, following Justin 's tutorial http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/index.html I have done the Umbrella Sampling simulations without using any restraints in any of the monomers, however, I can see that they move and gyrate so that although the c.o.m are separated from each other, there are parts of both interacting, in such way that they are not separated as they should be. Would it be correct if I apply restraints to both monomers in all the Umbrella Sampling simulations?. I have seen that in Justin's tutorial they applied restraints to one of the chains, but in my case I think I will need to restrain both of the units. Would that be correct for the PMF calculation? Thanks a lot in advance. Rebeca. > Date: Mon, 20 Jun 2011 17:03:56 -0400 > From: jalem...@vt.edu > To: rega...@hotmail.com > CC: gmx-users@gromacs.org > Subject: Re: doubt about your Umbrella Sampling tutorial > > > > Rebeca García Fandiño wrote: > > Dear Justin, > > my name is Rebeca and I am a postdoctoral student in Santiago de > > Compostela University. Sorry for disturbing you to your personal mail, I > > have tried to post to the Gromacs-list first, but I did not get any answer. > > I was traveling and not paying much attention to messages across the list. I > will CC this reply to the list in the hopes that it is useful to others, as > well. > > > I am trying to obtain the PMF from Umbrella Sampling of the process of > > separating two monomers of a dimer, following your tutorial, and I have > > a pair of doubts: > > > > 1)In this tutorial the generation of configurations is done using a .mdp > > file for pulling one chain from another, but is it possible to generate > > the configurations for Umbrella Sampling "by hand", I mean, changing the > > z coordinate of the monomer I want to move, then solvating and then > > minimizing these configurations? Is there any problem with this protocol > > for the obtaining of the configurations? > > > > No problem at all. The tutorial is but one possible method. > > > 2) I have noticed that you use restraints in the md_umbrella.mdp for the > > fixed chain. Is that correct? I can understand the restraints in the > > pulling simulations for generate starting configurations, but once you > > have the configurations, is is necessary to restrain one part of the > > system? > > > > Not usually. The tutorial presents a special case. > > > Thanks a lot in advance for your help with this topic, and thank you > > very much also for publishing this interesting tutorial. There was > > nothing useful until that for Umbrella Sampling with Gromacs 4.0, so I > > think it is more than wellcome for all Gromacs users! > > Glad they're useful :) > > -Justin > > > Best wishes, > > Rebeca. > > > > Dr. Rebeca García Fandiño > > Department of Organic Chemistry and Center for Research in Biological > > Chemistry > > and Molecular Materials > > Santiago de Compostela University > > E-15782 Santiago de Compostela (Spain) > > e-mail: rebeca.garcia.fand...@usc.es > > Phone: 34-981563100 ext 15760 > > > > > > > > > > > > > > > > -- > > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Generation of configurations for Umbrella Sampling
Hello, I am trying to obtain the PMF from Umbrella Sampling of the process of separating two monomers of a dimer. I am following the tutorial http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/05_pull.html and I have a doubt: In this tutorial the generation of configurations is done using a .mdp file for pulling one chain from another, but is it possible to generate the configurations for Umbrella Sampling "by hand", I mean, changing the z coordinate of the monomer I want to move, then solvating and then minimizing these configurations? Is there any problem with this protocol for the obtaining of the configurations? Thanks a lot for your help. Best wishes, Dr. Rebeca Garcia Santiago de Compostela University Spain -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] diffusion constant
Hello, I am trying to calculate the diffusion coefficient of a molecule in water using g_msd, and I have a doubt: I get 3 different values when I use the trajectory directly from the simulation, the trajectory using PBC conditions, and the "fitted trajectory". Which would be the correct value for the diffusion coefficient? Thanks a lot for your help in advance. Best wishes, Rebeca Garcia Organic Chemistry Department Santiago de Compostela University Spain -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] g_analyze with multiple sets
Thanks a lot for the clarification, now it works perfectly. Sorry for the confusion! Best wishes, Rebeca. > Date: Fri, 14 Jan 2011 13:46:26 -0500 > From: jalem...@vt.edu > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] g_analyze with multiple sets > > > > Rebeca García Fandiño wrote: > > Hello, > > I have several files containing two columns, x and y (x is the same for > > all of them). > > I would like to calculate the average and standar deviation (as the > > error bar) for the y column for all my data sets. > > I have tried using g_analyze: > > > > g_analyze -n 3 -av average.xvg -errbar stddev -f set1.xvg & set2.xvg & > > set3.xvg > > > > I get several errors: > > set2.xvg: Command not found > > set3.xvg: Command not found > > > > And also: "Set 2 is horter (0) than the previous set (1775) > > > > I have seen a similar error in the gromacs list archive, and the problem > > seemed to be the space before the &. I remove this whitespace and also > > the space after the &, but I get the same results. > > > > How could I solve this problem? > > > > g_analyze does not take multiple simultaneous input. The "&" referred to in > the > help text refers to data sets within the same .xvg file that are separated by > &. > > -Justin > > > Thanks a lot for your help in advance. > > > > Best wishes, > > > > Rebeca Garcia > > Postdoctoral student > > Santiago de Compostela University > > Spain > > rega...@hotmail.com > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > <#> > > > > > > > > > > > > > > <#> > > > > > > > > > > > > <#> > > > > > > <#> > > > > > > > > > > > > -- > > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > B
[gmx-users] g_analyze with multiple sets
Hello, I have several files containing two columns, x and y (x is the same for all of them). I would like to calculate the average and standar deviation (as the error bar) for the y column for all my data sets. I have tried using g_analyze: g_analyze -n 3 -av average.xvg -errbar stddev -f set1.xvg & set2.xvg & set3.xvg I get several errors: set2.xvg: Command not found set3.xvg: Command not found And also: "Set 2 is horter (0) than the previous set (1775) I have seen a similar error in the gromacs list archive, and the problem seemed to be the space before the &. I remove this whitespace and also the space after the &, but I get the same results. How could I solve this problem? Thanks a lot for your help in advance. Best wishes, Rebeca Garcia Postdoctoral student Santiago de Compostela University Spain rega...@hotmail.com
RE: [gmx-users] g_bundle question
OK,
you are right, I haven´t noticed the -z option!
I will try it.
Thanks a lot for your help.
Best wishes,
Rebeca.
> Date: Thu, 16 Dec 2010 15:34:05 -0500
> From: jalem...@vt.edu
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] g_bundle question
>
>
>
> Rebeca García Fandiño wrote:
> > Thanks for the suggestion.
> > However, I have one question. If I use g_sgangle I can calculate the
> > angle formed by the atoms at the top and bottom of my nanotube, but if
> > the nanotube is considered as a whole (as a rigid system), and it tilts,
> > then the result would not show the tilt respect to the z axis of the
> > membrane, am I right?
>
> Maybe I'm not clear on what you want. I haven't used g_sgangle much, but it
> seems to me that option -oa ("Angle between the two groups specified in the
> index file") would do what you want. Otherwise, g_sgangle -z might.
>
> -Justin
>
> > Thanks a lot for your help.
> > Best wishes,
> > Rebeca.
> >
> > > Date: Thu, 16 Dec 2010 11:59:38 -0500
> > > From: jalem...@vt.edu
> > > To: gmx-users@gromacs.org
> > > Subject: Re: [gmx-users] g_bundle question
> > >
> > >
> > >
> > > Rebeca García Fandiño wrote:
> > > > Hello,
> > > > I am trying to calculate the tilt angle of the principal axis of a
> > > > nanotube inserted into a membrane using g_bundle. In the index file I
> > > > have selected a group of atoms at the top and a group of atoms at the
> > > > bottom of the nanotube, and I using the option -na 1 and -z to
> > calculate
> > > > the tilt respect to the z axis of the membrane.
> > > > I suppose that the results I have obtained in bun_tilt.xvg are the
> > tilt
> > > > angles respect to the average axis (along the simulation), is that
> > > > right? Is there any way to calculate the tilt angle respect to a
> > > > reference axis (for example, the axis formed by the 2 groups in the
> > > > index file in the first structure, which is just perpendicular to the
> > > > membrane?
> > >
> > > Sounds like something g_sgangle can do.
> > >
> > > -Justin
> > >
> > > > Thanks a lot in advance for your help.
> > > > Best wishes,
> > > >
> > > > Rebeca Garcia
> > > > Santiago de Compostela University
> > > > Spain
> > > > rega...@hotmail.com
> > > >
> > >
> > > --
> > >
> > >
> > > Justin A. Lemkul
> > > Ph.D. Candidate
> > > ICTAS Doctoral Scholar
> > > MILES-IGERT Trainee
> > > Department of Biochemistry
> > > Virginia Tech
> > > Blacksburg, VA
> > > jalemkul[at]vt.edu | (540) 231-9080
> > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> > >
> > >
> > > --
> > > gmx-users mailing list gmx-users@gromacs.org
> > > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > > Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> > > Please don't post (un)subscribe requests to the list. Use the
> > > www interface or send it to gmx-users-requ...@gromacs.org.
> > > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> --
>
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
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RE: [gmx-users] g_bundle question
Thanks for the suggestion. However, I have one question. If I use g_sgangle I can calculate the angle formed by the atoms at the top and bottom of my nanotube, but if the nanotube is considered as a whole (as a rigid system), and it tilts, then the result would not show the tilt respect to the z axis of the membrane, am I right? Thanks a lot for your help. Best wishes, Rebeca. > Date: Thu, 16 Dec 2010 11:59:38 -0500 > From: jalem...@vt.edu > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] g_bundle question > > > > Rebeca García Fandiño wrote: > > Hello, > > I am trying to calculate the tilt angle of the principal axis of a > > nanotube inserted into a membrane using g_bundle. In the index file I > > have selected a group of atoms at the top and a group of atoms at the > > bottom of the nanotube, and I using the option -na 1 and -z to calculate > > the tilt respect to the z axis of the membrane. > > I suppose that the results I have obtained in bun_tilt.xvg are the tilt > > angles respect to the average axis (along the simulation), is that > > right? Is there any way to calculate the tilt angle respect to a > > reference axis (for example, the axis formed by the 2 groups in the > > index file in the first structure, which is just perpendicular to the > > membrane? > > Sounds like something g_sgangle can do. > > -Justin > > > Thanks a lot in advance for your help. > > Best wishes, > > > > Rebeca Garcia > > Santiago de Compostela University > > Spain > > rega...@hotmail.com > > > > -- > > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] g_bundle question
Hello, I am trying to calculate the tilt angle of the principal axis of a nanotube inserted into a membrane using g_bundle. In the index file I have selected a group of atoms at the top and a group of atoms at the bottom of the nanotube, and I using the option -na 1 and -z to calculate the tilt respect to the z axis of the membrane. I suppose that the results I have obtained in bun_tilt.xvg are the tilt angles respect to the average axis (along the simulation), is that right? Is there any way to calculate the tilt angle respect to a reference axis (for example, the axis formed by the 2 groups in the index file in the first structure, which is just perpendicular to the membrane? Thanks a lot in advance for your help. Best wishes, Rebeca Garcia Santiago de Compostela University Spain rega...@hotmail.com -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Ramachandran plot for non standar residues
Hello, I am trying to calculate the Ramachandran plot for a molecules based on non-standar aminoacids, parametrized with the Gaff force field and simulated with Gromacs 4.0.7. When I try using g_rama -f trajectory.xtc -s topology.tpr -o rama.xvy I get: Found 0 phi-psi combinations. I suppose the problem is the nomenclature of my atoms, since I don´t have any CA named atoms. Is there any way to calculate g_rama for non-standar residues defining the atoms I need? Thanks a lot for your help. Best whishes, Rebeca Garcia Santiago de Compostela University Spain -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] g_rama problem about dihedrals
Hello, I have an old trajectory simulated using the Charmm force field and I would like to get the Phi/Psi dihedral combinations as a function of time, using g_raman. I am using a single pdb to start with. I created a topology for this pdb using: pdb2gmx -f protein.pdb -o protein_gmx.pdb -p topol.top (and selecting 8: CHARMM27 all-atom force field (with CMAP) - version 2.0beta) Then, I generated a .tpr file using grompp and I used the g_raman tool: g_rama -f protein_gmx.gro -s topology.tpr -o rama.xvg I get a file called rama.xvg with a pair value for each residue (except for the terminal ones), that is something like: @ s0 symbol 2 @ s0 symbol size 0.4 @ s0 symbol fill 1 -83.2716 85.9943 LYS-2 -89.0885 36.4162 ILE-3 -91.7006 61.4224 GLY-4 (...) But I get a lot of messages saying: Reading file topology.tpr, VERSION 4.5 (single precision) Found 166 phi-psi combinations Dihedral around 24,26 not found in topology. Using mult=3 Dihedral around 26,44 not found in topology. Using mult=3 Dihedral around 46,48 not found in topology. Using mult=3 Dihedral around 48,63 not found in topology. Using mult=3 Dihedral around 65,67 not found in topology. Using mult=3 (...) Dihedral around 2526,2528 not found in topology. Using mult=3 Dihedral around 2528,2544 not found in topology. Using mult=3 Dihedral around 2546,2548 not found in topology. Using mult=3 Dihedral around 2548,2551 not found in topology. Using mult=3 I have seen there are other people in the Gromacs list that have asked about this question, but I could not find any help from the answers there. Any help will be very appreciated! Thanks a lot in advance, Rebeca Garcia Universidad de Santiago de Compostela Spain rega...@hotmail.com -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] topology for a cyclic peptide
Hi, I am trying to get the topology of a cyclic peptide, but when I try to do pdb2pgx I get automatically the correction to a terminal one. I have looked in the Gromacs list and I only have found a entry about it, http://osdir.com/ml/science.biology.gromacs.user/2006-08/msg00297.html but I cannot find a solution from there. Does anyone have any idea about it, please? Thanks a lot for your help. Best wishes, Rebeca García Santiago de Compostela University Spain _ No has visto nada como el nuevo Messenger, ¡te sorprenderá! http://explore.live.com/windows-live-messenger-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] problem in g_rdf using only x and y
Thank you very much. One question, how should I use it? Should I compile Gromacs again? Cheers, Rebeca. From: g...@hotmail.com To: jalem...@vt.edu; gmx-users@gromacs.org Subject: RE: [gmx-users] problem in g_rdf using only x and y Date: Wed, 24 Feb 2010 15:29:49 +0100 CC: Hi, I realize now that I committed a fix for this bug 3 days after the release of 4.0.7 (and not 3 days before the release as I initially thought). If you need it right now, I put the fixed source at: http://hess.cbr.su.se/~hess/gmx_rdf.c Berk > Date: Wed, 24 Feb 2010 06:52:57 -0500 > From: jalem...@vt.edu > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] problem in g_rdf using only x and y > > > > Berk Hess wrote: > > Well, I fixed a bug with g_rdf -xy before the 4.0.7 release. > > But apparently this fix does not work under all conditions. > > Could one of you file a bugzilla and attach a tpr file and a trajectory, > > preferably with only one or very few frames and write the exact command > > line? > > Filed as bugzilla #399. I uploaded a .tpr and .gro that reproduce the error; > if > you want an actual (small) trajectory, I can provide that as well. > > -Justin > > > > > Thanks, > > > > Berk > > > > > Date: Tue, 23 Feb 2010 13:51:39 -0500 > > > From: jalem...@vt.edu > > > To: gmx-users@gromacs.org > > > Subject: Re: [gmx-users] problem in g_rdf using only x and y > > > > > > > > > > > > Rebeca García Fandiño wrote: > > > > Hi, > > > > thank you very much for your answer. However, I have tried with the > > > > 4.0.7 version, and the problem continues, and it is just the same. I > > > > have the trajectory and tpr file obtained with the 4.0.4 version. > > Do you > > > > think it cares, or maybe is it another problem? > > > > > > I think there is a problem in g_rdf, not a 4.0.4 vs 4.0.7 issue. I > > was actually > > > about to report this problem, myself. I have simulations that I did with > > > version 4.0.7, and the RDF analysis hung the exact same way as you > > reported. > > > > > > -Justin > > > > > > > Cheers, > > > > Rebeca. > > > > > > > > > > > > > > From: g...@hotmail.com > > > > To: gmx-users@gromacs.org > > > > Subject: RE: [gmx-users] problem in g_rdf using only x and y > > > > Date: Tue, 23 Feb 2010 16:47:43 +0100 > > > > > > > > Hi, > > > > > > > > I fixed this bug in 4.0.7. > > > > > > > > Berk > > > > > > > > > > > > > > From: rega...@hotmail.com > > > > To: gmx-users@gromacs.org > > > > Date: Tue, 23 Feb 2010 15:40:07 + > > > > Subject: [gmx-users] problem in g_rdf using only x and y > > > > > > > > Hi, > > > > I am trying to calculate g_rdf using only the x and y components of > > the > > > > distance (gromacs 4.0.4): > > > > > > > > g_rdf -f trajectory.xtc -s production1.tpr -n index.ndx -o > > rdf_Na_xy.xvg > > > > -com -norm -pbc -xy and the calculations stays at the window: > > > > > > > > Select a group: 1 > > > > Selected 1: 'UNK' > > > > Select a group: 4 > > > > Selected 4: 'Na' > > > > Reading frame 0 time 0.000 > > > > > > > > for days...(I had to kill it after 4 days). > > > > > > > > Using the same order without -xy takes only 10 minutes. > > > > > > > > Is there anything wrong with the commands I am using? Or maybe is > > there > > > > a bug in the -xy option? > > > > > > > > Thank you very much for your help, in advance. > > > > > > > > Best wishes, > > > > > > > > Rebeca Garcia. > > > > <http://serviciosmoviles.es.msn.com/hotmail/movistar.aspx> > > > > > > > > > > ¿Quieres tener a tus amigos de Facebook en Messenger? ¡Clic AQUÍ! > > > > <http://vivelive.com/feedfacebook/> > > > > > > > > > > New Wi
RE: [gmx-users] problem in g_rdf using only x and y
Hi, thank you very much for your answer. However, I have tried with the 4.0.7 version, and the problem continues, and it is just the same. I have the trajectory and tpr file obtained with the 4.0.4 version. Do you think it cares, or maybe is it another problem? Cheers, Rebeca. From: g...@hotmail.com To: gmx-users@gromacs.org Subject: RE: [gmx-users] problem in g_rdf using only x and y Date: Tue, 23 Feb 2010 16:47:43 +0100 Hi, I fixed this bug in 4.0.7. Berk From: rega...@hotmail.com To: gmx-users@gromacs.org Date: Tue, 23 Feb 2010 15:40:07 + Subject: [gmx-users] problem in g_rdf using only x and y Hi, I am trying to calculate g_rdf using only the x and y components of the distance (gromacs 4.0.4): g_rdf -f trajectory.xtc -s production1.tpr -n index.ndx -o rdf_Na_xy.xvg -com -norm -pbc -xy and the calculations stays at the window: Select a group: 1 Selected 1: 'UNK' Select a group: 4 Selected 4: 'Na' Reading frame 0 time0.000 for days...(I had to kill it after 4 days). Using the same order without -xy takes only 10 minutes. Is there anything wrong with the commands I am using? Or maybe is there a bug in the -xy option? Thank you very much for your help, in advance. Best wishes, Rebeca Garcia. ¿Quieres tener a tus amigos de Facebook en Messenger? ¡Clic AQUÍ! New Windows 7: Find the right PC for you. Learn more. _ Ibex 35, comparadores de hipotecas, Euribor, foros de bolsa. ¡Nuevo MSN Dinero! http://dinero.es.msn.com/-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] problem in g_rdf using only x and y
Hi, I am trying to calculate g_rdf using only the x and y components of the distance (gromacs 4.0.4): g_rdf -f trajectory.xtc -s production1.tpr -n index.ndx -o rdf_Na_xy.xvg -com -norm -pbc -xy and the calculations stays at the window: Select a group: 1 Selected 1: 'UNK' Select a group: 4 Selected 4: 'Na' Reading frame 0 time0.000 for days...(I had to kill it after 4 days). Using the same order without -xy takes only 10 minutes. Is there anything wrong with the commands I am using? Or maybe is there a bug in the -xy option? Thank you very much for your help, in advance. Best wishes, Rebeca Garcia. _ Los auténticos Hotmail y Messenger en tu Blackberry con Movistar. ¡Descárgatelos ya! http://serviciosmoviles.es.msn.com/messenger/blackberry.aspx-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] rmax and amax options of g_densmap
Hi, I would like to calculate the density maps for the water inside a pore that has a cilindrical shape, but not the water outside it, that is also present in the box. I don´t understand vey well the options of g_densmap "-amax" and "-rmax". With -amax I define the maximun axial distance from the center, let´s say the principal axis of my pore. With -rmax, I define the maximun radial distance, but is this in a perpendicular direction to the axis? or also in 3 directions? Because, if it is in 3 directions, and my pore is cilindrical (not spherical), so rmax >> amax, there will be a region that is not going to be taking into account for the density calculation... Could anybody explain a little more about rmax and amax options of g_densmap, please? Thank you very much in advance. Best wishes, Rebeca Garcia. _ Recibe las alertas Hotmail en tu móvil ¡Actívalas ya! http://home.mobile.live.com/MobileAttach.mvc/?mkt=es-es-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] different results in different machines
Thank you very much for the suggestions. I will look carefully for the convergence of my PMF to see if it is the problem. Cheers, Rebeca. From: x.peri...@rug.nl To: gmx-users@gromacs.org Subject: Re: [gmx-users] different results in different machines Date: Thu, 11 Feb 2010 20:00:32 +0100 On Feb 11, 2010, at 7:40 PM, Rebeca García Fandiño wrote:Hi, I am doing PMF calculations using Gromacs 3.3.3, and I have found very different results using 2 different machines. Attached you can see that the graphics are really different for both cases (about 10 KJ/mol!!). The version of Gromacs (3.3.3) and number of processors used (2) is the same for both calculations. The .tpr files and all the starting files are identical for both calculations. The only thing that changes is the machine where they were carried out. I have checked the energy files for both cases, and they are different, but taking into account the stochastic effect, I suppose it is normal. There are slight differences in the energies in the step 0 for some of the windows (but in the 5th decimal number, so they should not be important, I suppose). Well this might be a problem but the 5th decimal is pretty far. Any idea of the cause of the problem? Has anyone experienced similar problems? Any suggestion will be much appreciated. Thanks a lot for your help, in advance. the only thing you have left is that you have not sampled enought ... soyou have not reached convergence.Did you try to repeat the calculation on the ame machine changing the initial velocities ? Cheers, Rebeca Garcia Elige un juego de Messenger. Reta a un amigo. ¡Pruébalo ya! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php _ Ibex 35, comparadores de hipotecas, Euribor, foros de bolsa. ¡Nuevo MSN Dinero! http://dinero.es.msn.com/-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] different results in different machines
Hi, I am doing PMF calculations using Gromacs 3.3.3, and I have found very different results using 2 different machines. Attached you can see that the graphics are really different for both cases (about 10 KJ/mol!!). The version of Gromacs (3.3.3) and number of processors used (2) is the same for both calculations. The .tpr files and all the starting files are identical for both calculations. The only thing that changes is the machine where they were carried out. I have checked the energy files for both cases, and they are different, but taking into account the stochastic effect, I suppose it is normal. There are slight differences in the energies in the step 0 for some of the windows (but in the 5th decimal number, so they should not be important, I suppose). Any idea of the cause of the problem? Has anyone experienced similar problems? Any suggestion will be much appreciated. Thanks a lot for your help, in advance. Cheers, Rebeca Garcia _ ¿Aún no sabes qué móvil eres? ¡Descúbrelo aquí! http://www.quemovileres.com/ comparation_neuron_ngs.pdf Description: Adobe PDF document -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] options in mdp for PMF
Hi, I would like to calculate the PMF of an ion along a channel using Gromacs 4, and I have a doubt about the options I should use in the .mdp file: -which option should I choose for pull_geometry: distance? direction? or position? -which is the equivalent option to the old "Pos1" (in Gromacs 3) for the Gromacs 4 version? Thank you very much for your help. Best wishes, Rebeca Garcia Fandiño Oxford Universtity UK _ Deja que Sietes te enseñe todo los secretos de Windows http://www.sietesunpueblodeexpertos.com/___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] PMF and Gromacs 4
Hi, I am trying to calculate the PMF of an ion with Gromacs 4. I have read in the Gromacs list that the pull code had been completely rewritten in the new version of Gromacs, but I cannot find much information about the new way to use this. Reading the manual (pag 280) I can see: “The options -pi, -po, -pd, -pn are used for potential of mean force calculations and umbrella sampling. See manual.” So, I prepared a tpr and a .ppa file and tried the calculation and used (for example for one window): source /gpfs/apps/GROMACS/gromacs-4.0.2/bin/GMXRC srun -n 8 mdrun_s -v -stepout 1000 -s NA-0.0250.tpr -pi NA-0.0250.ppa -po pullout.ppa -pn NA-0.0250.ndx -pd -deffnm NA-0.0250 gzip NA-0.0250.pdo Being NA-0.0250.ppa: verbose = yes runtype = umbrella pulldim = N N Y reftype = com reference_group = UNK group_1 = Na_-0.025 K1= 970.86; ; kJ / (mol nm^2) Pos1 = 0.000 0.000 -0.025 ; centre of the umbrella potential I don´t get any errors during the calculation, however, I did not get any out files such as *.pdo. I only get the *cpt, *trr, *log and *edr files after the calculation, but no signal of *pdo. Does anyboy had used Gromacs 4 for calculating PMF? Am I doing something wrong? Thank you very much for your help. Best wishes, Rebeca Garcia. Santiago de Compostela University Spain. Entra al Nuevo Canal Motor y descubre por qué los coches más rápidos sólo aparcan en MSN. Nuevo diseño, más completo y abierto a tu opinión. ¡Nuevo Canal Motor! _ ¿Estás fuera de temporada? Entra ya en Nueva Temporada y entérate antes que nadie de sobre famosos, moda, belleza y el look que se lleva este otoño. http://events.es.msn.com/entretenimiento/nueva-temporada/vuelta-al-cole/___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] PMF in Gromacs 4
Hi, I am trying to calculate the PMF of an ion with Gromacs 4. I have read in the Gromacs list that the pull code had been completely rewritten in the new version of Gromacs, but I cannot find much information about the new way to use this. Reading the manual (pag 280) I can see: “The options -pi, -po, -pd, -pn are used for potential of mean force calculations and umbrella sampling. See manual.” So, I prepared a tpr and a .ppa file and tried the calculation and used (for example for one window): source /gpfs/apps/GROMACS/gromacs-4.0.2/bin/GMXRC srun -n 8 mdrun_s -v -stepout 1000 -s NA-0.0250.tpr -pi NA-0.0250.ppa -po pullout.ppa -pn NA-0.0250.ndx -pd -deffnm NA-0.0250 gzip NA-0.0250.pdo Being NA-0.0250.ppa: verbose = yes runtype = umbrella pulldim = N N Y reftype = com reference_group = UNK group_1 = Na_-0.025 K1= 970.86; ; kJ / (mol nm^2) Pos1 = 0.000 0.000 -0.025 ; centre of the umbrella potential I don´t get any errors during the calculation, however, I did not get any out files such as *.pdo. I only get the *cpt, *trr, *log and *edr files after the calculation, but no signal of *pdo. Does anyboy had used Gromacs 4 for calculating PMF? Am I doing something wrong? Thank you very much for your help. Best wishes, Rebeca Garcia. Santiago de Compostela University Spain. _ Convierte las fotos que más te gustan en tu nuevo fondo de escritorio para el ordenador. Es fácil y además gratis http://wallpapers.msn.com/es-es___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] planar geometry: dummy atoms or angle restraints?
Hi, I am trying to simulate an organic system which has a planar-square Pt center. To mantain the planar geometry of the metal, I have thought about 2 possibilities: -introduce 2 dummy atoms at the axial possitions of the metal; however, I get errors complaining about these extra atoms has mass 0. I have read the manual and also looked at the GMX list, and I have found that other people have also found problems of these type. I have read that in case such as acetonitrile the advice was to redistribute the mass over N and CH3 such that centre of mass is unchanged and inertia tensor is not modified too much either. Should I do something similar in my case? Which mass should I redistribute? The mass of the whole molecule? -increase the harmonic restraints for angles where the metal is involved. Would this approximation would be as correct as the one mentioned before or would it better to use dummy atoms? Thank you very much for your help in advance. Best wishes, Dr. Rebeca Garcia Universidad de A Coruña Spain _ ¿Quieres ver los mejores videos de MSN? Enciende Messenger TV http://messengertv.msn.com/mkt/es-es/default.htm___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] dummy atoms in planar square Pt
Hi, I am trying to simulate an organic system which has a planar-square Pt center. I am following the methodology employed in JACS 2008, 10040 (where they use amber calculations). There, they use 2 dummy atoms to mantain the planar square geometry of the metal. I have built my system with no dummy atoms, using GAFF and converted it into Gromacs, so now I have a .gro and a .top file. I have introduced then the dummy atoms, in the .gro and in the topology file, but I get errors complaining about these extra atoms has mass 0. I have read the manual and also looked at the GMX list, and I have found that other people have also found problems of these type. I have read that in case such as acetonitrile the advice was to redistribute the mass over N and CH3 such that centre of mass is unchanged and inertia tensor is not modified too much either. Should I do something similar in my case? Which mass should I redistribute? The mass of the whole molecule? Thank you very much for your help. Best wishes, Dr. Rebeca Garcia Universidad de A Coruña Spain _ ¿Quieres ver los mejores videos de MSN? Enciende Messenger TV http://messengertv.msn.com/mkt/es-es/default.htm___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] problem fitting trajectory
Hello, I have done a simulation using Gromacs 4 (4.0.2) and I would like to have a trajectory were the protein is fitted to the first structure (to mantain the exact orientation). When I have tried echo 1 1 0 | trjconv -f production_1_3.xtc -s production1.tpr -center -fit rot+trans -pbc mol -o production_1_3_fit.xtc visualizing production_1_3_fit.xtc I can see that the protein is fitted, however there are a lot of "holes" into the water box. It seems like the pbc were not correctly applied. I have tried changing a lot of options (-pbc res, -boxcenter rect,...) but nothing works. The options trjconv -f production_1_3.xtc -s production1.tpr -center -boxcenter rect -fit rot+trans -pbc mol -o production_1_3_fit.xtc do not produce any hole in the box of water, but the box entirely moves around the protein, and sometimes it is outside of it and not solvated. I have also tried using Gromacs 4.0.4, but the problem is still the same. Could anybody give an idea of how solving it, please? Thank you very much for your help. Best wishes, Rebeca Garcia Academic Visitor Oxford University _ Chatea sin límites en Messenger con la tarifa plana de Orange http://serviciosmoviles.es.msn.com/messenger/orange.aspx___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] Re: goverrriding problem
Thank you very much, Alan. In this case, I am not using acpypi, since I am using a topology for dopc already published, and it is already converted into Gromacs. So, it´s manually, as you suppose. I will follow your suggestion and change c and o by c_ and o_. Best wishes, Rebeca. From: alanwil...@gmail.com Date: Thu, 4 Jun 2009 22:19:30 +0100 To: gmx-users@gromacs.org Subject: [gmx-users] Re: goverrriding problem Yep, contrary to AMBER, GMX is not case sensitive, so C and c are the same and since you declare them twice you get this overriding warning. However, I did acpypi aware of this (it should add '_' to e.g. c, making 'c_'). Unless you're doing something manually (as it seems). Otherwise it would a pleasure to see this issue closely (can you send me your input prmtop and inpcrd?). Otherwise do it yourself by making c_ and o_ and the overriding warn will be off. Cheers, Alan Message: 7 Date: Thu, 4 Jun 2009 20:55:52 + From: Rebeca Garc?a Fandi?o Subject: [gmx-users] overrriding problem To: Message-ID: Content-Type: text/plain; charset="iso-8859-1" Hi, I am doing a simulation combining amber and Gaff force field (for dopc lipids), this is the first part of my topology file: ; UNK_GMX.top created by acpypi on Thu Jun 4 22:06:03 2009 [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ 1 2 yes 0.5 0.8333 [ atomtypes ] ;name bond_type mass charge ptype sigma epsilon Amb CA CA 0.0 0.0 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 CT CT 0.0 0.0 A 3.39967e-01 4.57730e-01 ; 1.91 0.1094 CC 0.0 0.0 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 HO HO 0.0 0.0 A 0.0e+00 0.0e+00 ; 0.00 0. OO 0.0 0.0 A 2.95992e-01 8.78640e-01 ; 1.66 0.2100 OH OH 0.0 0.0 A 3.06647e-01 8.80314e-01 ; 1.72 0.2104 c3c3 12.0100-0.12654 A3.399676e-01 4.577296e-01 ; 1.91 0.1094 hchc1.0080 0.02245 A2.649538e-01 6.568880e-02 ; 1.49 0.0157 c2c2 12.0100-0.15458 A3.399676e-01 3.598240e-01 ; 1.91 0.0860 haha1.0080 0.11146 A2.599647e-01 6.276000e-02 ; 1.46 0.0150 c c12.0100 0.44800A3.399676e-01 3.598240e-01 ; 1.91 0.0860 o o 16.-0.47180 A2.959927e-01 8.786400e-01 ; 1.66 0.2100 osos 16.-0.15429 A3.18e-01 7.112800e-01 ; 1.68 0.1700 h1h1 1.0080 0.16551A2.471358e-01 6.568880e-02 ; 1.39 0.0157 p5p5 30.9700 1.14364A3.741781e-01 8.368000e-01 ; 2.10 0.2000 n4n4 14.0100 0.01626 A3.250004e-01 7.112800e-01 ; 1.82 0.1700 hxhx1.0080 0.08244 A1.959981e-01 6.568880e-02 ; 1.10 0.0157 OWOW 0.0 0.0 A 3.16572e-01 6.49775e-01 ; 1.78 0.1553 HWHW 0.0 0.0 A 0.0e+00 0.0e+00 ; 0.00 0. NaNa 0.0 0.0 A 2.15954e-01 1.47545e+00 ; 1.21 0.3526 ClCl 0.0 0.0 A 4.83045e-01 5.34924e-02 ; 2.71 0.0128 When I try to minimize the system, with grompp -f minimizado.mdp -c final_system.gro -p final_system.top -o minimizado.tpr I find 2 warnings: WARNING 1 [file final_system.top, line 19]: Overriding atomtype c WARNING 2 [file final_system.top, line 20]: Overriding atomtype o It is like it is not distinguing the capitals for amber and non-capitals for gaff. Does anybody know which can be the cause of these warnings? Thank you very much, Rebeca Garcia University of Oxford -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. >>http://www.bio.cam.ac.uk/~awd28<< _ ¿Quieres ver los mejores videos de MSN? Enciende Messenger TV http://messengertv.msn.com/mkt/es-es/default.htm___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] overrriding problem
Hi, I am doing a simulation combining amber and Gaff force field (for dopc lipids), this is the first part of my topology file: ; UNK_GMX.top created by acpypi on Thu Jun 4 22:06:03 2009 [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ 1 2 yes 0.5 0.8333 [ atomtypes ] ;name bond_type mass charge ptype sigma epsilon Amb CA CA 0.0 0.0 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 CT CT 0.0 0.0 A 3.39967e-01 4.57730e-01 ; 1.91 0.1094 CC 0.0 0.0 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 HO HO 0.0 0.0 A 0.0e+00 0.0e+00 ; 0.00 0. OO 0.0 0.0 A 2.95992e-01 8.78640e-01 ; 1.66 0.2100 OH OH 0.0 0.0 A 3.06647e-01 8.80314e-01 ; 1.72 0.2104 c3c3 12.0100-0.12654 A3.399676e-01 4.577296e-01 ; 1.91 0.1094 hchc1.0080 0.02245 A2.649538e-01 6.568880e-02 ; 1.49 0.0157 c2c2 12.0100-0.15458 A3.399676e-01 3.598240e-01 ; 1.91 0.0860 haha1.0080 0.11146 A2.599647e-01 6.276000e-02 ; 1.46 0.0150 c c12.0100 0.44800A3.399676e-01 3.598240e-01 ; 1.91 0.0860 o o 16.-0.47180 A2.959927e-01 8.786400e-01 ; 1.66 0.2100 osos 16.-0.15429 A3.18e-01 7.112800e-01 ; 1.68 0.1700 h1h1 1.0080 0.16551A2.471358e-01 6.568880e-02 ; 1.39 0.0157 p5p5 30.9700 1.14364A3.741781e-01 8.368000e-01 ; 2.10 0.2000 n4n4 14.0100 0.01626 A3.250004e-01 7.112800e-01 ; 1.82 0.1700 hxhx1.0080 0.08244 A1.959981e-01 6.568880e-02 ; 1.10 0.0157 OWOW 0.0 0.0 A 3.16572e-01 6.49775e-01 ; 1.78 0.1553 HWHW 0.0 0.0 A 0.0e+00 0.0e+00 ; 0.00 0. NaNa 0.0 0.0 A 2.15954e-01 1.47545e+00 ; 1.21 0.3526 ClCl 0.0 0.0 A 4.83045e-01 5.34924e-02 ; 2.71 0.0128 When I try to minimize the system, with grompp -f minimizado.mdp -c final_system.gro -p final_system.top -o minimizado.tpr I find 2 warnings: WARNING 1 [file final_system.top, line 19]: Overriding atomtype c WARNING 2 [file final_system.top, line 20]: Overriding atomtype o It is like it is not distinguing the capitals for amber and non-capitals for gaff. Does anybody know which can be the cause of these warnings? Thank you very much, Rebeca Garcia University of Oxford _ Nuevo Windows Live, un mundo lleno de posibilidades. Descúbrelo. http://www.microsoft.com/windows/windowslive/default.aspx___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] spc.itp for the amber force field
Hi, I am trying to simulate a system using the parameters for ions developed by Joung et al. and implemented in Amber (frcmod.ionsjc_spce). I have the topology and the crd file. Now, I want to obtain the topology for Gromacs using amb2gmx.pl, so I must change the default parameters (for tip3p) included in amb2gmx.pl. I have seen that in the .tar file ffamber_v4.0 there is no a corresponding itp file for spc model of water in amber, so what parameters should I include for the section of bondtypes, angletypes, atoms, bonds, angles, settles,...? Those corresponding to the SCP in Gromacs directly? Thank you very much for your help. Best wishes, Rebeca Garcia Academic Visitor Oxford University _ Chatea sin límites en Messenger con la tarifa plana de Orange http://serviciosmoviles.es.msn.com/messenger/orange.aspx___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] crystals of KCl during simulation
Thank you very much for your answers. Anyway, if I want to simulate my protein
with Amber, would it be a big problem to combine parameter from Amber with
parameters from OPLS for water and/or ions?
Best wishes,
Rebeca.
> Date: Tue, 2 Jun 2009 09:51:12 -0300
> Subject: Re: [gmx-users] crystals of KCl during simulation
> From: mo...@ufscar.br
> To: gmx-users@gromacs.org
>
> Hi Rebeca,
>
> the paper David suggests is certainly more complete, I just compared OPLS
> and Aqvist's parameters for sodium for the specific case of anionic
> micelles. anyway, if want to try the Aqvist's parameters take a look
> inside ffoplsaa.atp file (opls_408 for K+).
>
> best regards,
>
> André
>
> > Rebeca García Fandiño wrote:
> >>
> >> Thank you very much, André. Could you please indicate me how could
> >> I use these parameters in Gromacs? I have not seen them included in
> >> ions.itp and I could not find anything in the manual.
> >> Best wishes,
> >> Rebeca.
> >
> >
> > I would recommend reading the following paper, even though it only is
> > about NaCl it compares the properties of four different parameter sets,
> > and IIRC Åqvist's parameters were not so great.
> >
> > @Article{ Hess2006c,
> > author = "B. Hess and C. Holm and N. {van der Vegt}",
> > title = "Osmotic coefficients of atomistic NaCl (aq) force
> > fields",
> > journal = "J. Chem. Phys.",
> > year = 2006,
> > volume = 124,
> > pages = 164509,
> > abstract = "Solvated ions are becoming increasingly important
> > for (bio)molecular simulations. But there are not
> > much suitable data to validate the
> > intermediate-range solution structure that ion-water
> > force fields produce. We compare six selected
> > combinations of four biomolecular Na-Cl force fields
> > and four popular water models by means of effective
> > ion-ion potentials. First we derive an effective
> > potential at high dilution from simulations of two
> > ions in explicit water. At higher ionic
> > concentration multibody effects will become
> > important. We propose to capture those by employing
> > a concentration dependent dielectric
> > permittivity. With the so obtained effective
> > potentials we then perform implicit solvent
> > simulations. We demonstrate that our effective
> > potentials accurately reproduce ion-ion coordination
> > numbers and the local structure. They allow us
> > furthermore to calculate osmotic coefficients that
> > can be directly compared with experimental data. We
> > show that the osmotic coefficient is a sensitive and
> > accurate measure for the effective ion-ion
> > interactions and the intermediate-range structure of
> > the solution. It is therefore a suitable and useful
> > quantity for validating and parametrizing atomistic
> > ion-water force fields. (c) 2006 American Institute
> > of Physics. 0021-9606"
> > }
> >
> >
> >
> >>
> >>
> >> > Date: Mon, 1 Jun 2009 14:52:35 -0300
> >> > Subject: RE: [gmx-users] crystals of KCl during simulation
> >> > From: mo...@ufscar.br
> >> > To: gmx-users@gromacs.org
> >> >
> >> > Hi Rebeca,
> >> >
> >> > I found out a few years ago that OPLS parameters for Na+ were
> >> inadequate
> >> > for my simulations on surfactants aggregation due to the formation of
> >> > stable (and unrealistic) ionic bridges. I got better structures using
> >> > Aqvist's parameters (available in GROMACS), maybe you could try these
> >> > parameters for K+ as well.
> >> >
> >> > please let me know if that works.
> >> >
> >> > best regards,
> >> >
> >> > André
> >> >
> >> >
> >> > >
> >> > > Yes, I use PME.
> >> > >
> >> > >> Date: Mon, 1 Jun 2009 19:34:27 +0200
> >> > >> From: sp...@xray.bmc.uu.se
> >> > >> To: gmx-users@gromacs.org
> >> > >> Subject: Re: [gmx-users] crystals of KCl during simulation
> >> > >>
> >> > >> Rebeca García Fandiño wrote:
> >> > >> > Thank you very much for your answer. I have read some recent
> >> > >> literature,
> >> > >> > and you are right, it is a problem about the parameters for ions
> >> in
> >> > >> Amber.
> >> > >> >
> >> &
RE: [gmx-users] crystals of KCl during simulation
Thank you very much, André. Could you please indicate me how could I use these parameters in Gromacs? I have not seen them included in ions.itp and I could not find anything in the manual. Best wishes, Rebeca. > Date: Mon, 1 Jun 2009 14:52:35 -0300 > Subject: RE: [gmx-users] crystals of KCl during simulation > From: mo...@ufscar.br > To: gmx-users@gromacs.org > > Hi Rebeca, > > I found out a few years ago that OPLS parameters for Na+ were inadequate > for my simulations on surfactants aggregation due to the formation of > stable (and unrealistic) ionic bridges. I got better structures using > Aqvist's parameters (available in GROMACS), maybe you could try these > parameters for K+ as well. > > please let me know if that works. > > best regards, > > André > > > > > > Yes, I use PME. > > > >> Date: Mon, 1 Jun 2009 19:34:27 +0200 > >> From: sp...@xray.bmc.uu.se > >> To: gmx-users@gromacs.org > >> Subject: Re: [gmx-users] crystals of KCl during simulation > >> > >> Rebeca García Fandiño wrote: > >> > Thank you very much for your answer. I have read some recent > >> literature, > >> > and you are right, it is a problem about the parameters for ions in > >> Amber. > >> > > >> > I have found this paper: > >> > Parameters of Monovalent Ions in the Amber-99 Forcefield: Assesment of > >> > Inaccuracies and Proposed Improvements > >> > http://pubs.acs.org/doi/abs/10.1021/jp0765392 > >> > > >> > There, they simulate nucleic acids using a combination of Amber and > >> > OPLS sigma and epsilon for the ions. I have tried that in the case of > >> my > >> > protein, just changing the ion sigma and epsilon in the topology by > >> > those corresponding to OPLS, but I still observe aggregation for the > >> ions. > >> > > >> > Would this combination of Amber and OPLS have any kind of potential > >> > problem during the simulation? Has anybody any idea to avoid this type > >> > of artefact? > >> > >> Just checking, do you use PME? (You should...) > >> > > >> > Thank you very much in advance, > >> > > >> > Rebeca. > >> > > >> > > To: gmx-users@gromacs.org > >> > > Subject: Re: [gmx-users] crystals of KCl during simulation > >> > > Date: Mon, 1 Jun 2009 14:34:55 +0200 > >> > > From: baa...@smplinux.de > >> > > > >> > > > >> > > Hi, > >> > > > >> > > rega...@hotmail.com said: > >> > > >> [..] but after equilibration I have observed that KCl is > >> > aggregating, like > >> > > >> if it was making crystals. When I used NaCl instead KCl, this not > >> > > >> happened. > >> > > > >> > > >> Does anybody has any idea about the reason of the behaviour of > >> KCl in > >> > > >> the simulation? > >> > > > >> > > This even does happen with Amber :) So my guess is you correctly > >> > transferred > >> > > the parameters, but stumbled upon an artefact. If you check the > >> recent > >> > > literature you may notice that many publications with Amber using K+ > >> > > only employ minimal (neutralising) salt conditions as a workaround. > >> At > >> > > least this is what we did recently [1]. > >> > > > >> > > Marc Baaden > >> > > > >> > > [1] Interactions between neuronal fusion proteins explored by > >> molecular > >> > > dynamics, Biophys.J.94, 2008, 3436-3446. > >> > > http://dx.doi.org/10.1529/biophysj.107.123117 > >> > > > >> > > -- > >> > > Dr. Marc Baaden - Institut de Biologie Physico-Chimique, Paris > >> > > mailto:baa...@smplinux.de - http://www.baaden.ibpc.fr > >> > > FAX: +33 15841 5026 - Tel: +33 15841 5176 ou +33 609 843217 > >> > > > >> > > > >> > > ___ > >> > > gmx-users mailing list gmx-users@gromacs.org > >> > > http://www.gromacs.org/mailman/listinfo/gmx-users > >> > > Please search the archive at http://www.gromacs.org/search before > >> > posting! > >> > > Please don't post (un)subscribe requests to the list. Use the > >> > > www
RE: [gmx-users] crystals of KCl during simulation
Yes, I use PME. > Date: Mon, 1 Jun 2009 19:34:27 +0200 > From: sp...@xray.bmc.uu.se > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] crystals of KCl during simulation > > Rebeca García Fandiño wrote: > > Thank you very much for your answer. I have read some recent literature, > > and you are right, it is a problem about the parameters for ions in Amber. > > > > I have found this paper: > > Parameters of Monovalent Ions in the Amber-99 Forcefield: Assesment of > > Inaccuracies and Proposed Improvements > > http://pubs.acs.org/doi/abs/10.1021/jp0765392 > > > > There, they simulate nucleic acids using a combination of Amber and > > OPLS sigma and epsilon for the ions. I have tried that in the case of my > > protein, just changing the ion sigma and epsilon in the topology by > > those corresponding to OPLS, but I still observe aggregation for the ions. > > > > Would this combination of Amber and OPLS have any kind of potential > > problem during the simulation? Has anybody any idea to avoid this type > > of artefact? > > Just checking, do you use PME? (You should...) > > > > Thank you very much in advance, > > > > Rebeca. > > > > > To: gmx-users@gromacs.org > > > Subject: Re: [gmx-users] crystals of KCl during simulation > > > Date: Mon, 1 Jun 2009 14:34:55 +0200 > > > From: baa...@smplinux.de > > > > > > > > > Hi, > > > > > > rega...@hotmail.com said: > > > >> [..] but after equilibration I have observed that KCl is > > aggregating, like > > > >> if it was making crystals. When I used NaCl instead KCl, this not > > > >> happened. > > > > > > >> Does anybody has any idea about the reason of the behaviour of KCl in > > > >> the simulation? > > > > > > This even does happen with Amber :) So my guess is you correctly > > transferred > > > the parameters, but stumbled upon an artefact. If you check the recent > > > literature you may notice that many publications with Amber using K+ > > > only employ minimal (neutralising) salt conditions as a workaround. At > > > least this is what we did recently [1]. > > > > > > Marc Baaden > > > > > > [1] Interactions between neuronal fusion proteins explored by molecular > > > dynamics, Biophys.J.94, 2008, 3436-3446. > > > http://dx.doi.org/10.1529/biophysj.107.123117 > > > > > > -- > > > Dr. Marc Baaden - Institut de Biologie Physico-Chimique, Paris > > > mailto:baa...@smplinux.de - http://www.baaden.ibpc.fr > > > FAX: +33 15841 5026 - Tel: +33 15841 5176 ou +33 609 843217 > > > > > > > > > ___ > > > gmx-users mailing list gmx-users@gromacs.org > > > http://www.gromacs.org/mailman/listinfo/gmx-users > > > Please search the archive at http://www.gromacs.org/search before > > posting! > > > Please don't post (un)subscribe requests to the list. Use the > > > www interface or send it to gmx-users-requ...@gromacs.org. > > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > > > ¿Eres del Madrid, del Barça, del Atleti...? Apoya a tu equipo en la Zona > > Fan de MSN Deportes > > <http://opiniones.msn.es/default.aspx/Futbol/Atletico-de-Madrid > > > > > > > > > > > ___ > > gmx-users mailing list gmx-users@gromacs.org > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at http://www.gromacs.org/search before posting! > > Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to gmx-users-requ...@gromacs.org. > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > -- > David. > > David van der Spoel, PhD, Professor of Biology > Dept. of Cell and Molecular Biology, Uppsala University. > Husargatan 3, Box 596, 75124 Uppsala, Sweden > phone: 46 18 471 4205 fax: 46 18 511 755 > sp...@xray.bmc.uu.se sp...@gromacs.org http://folding.bmc.uu.se > > ___ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs
RE: [gmx-users] crystals of KCl during simulation
Thank you very much for your answer. I have read some recent literature, and you are right, it is a problem about the parameters for ions in Amber. I have found this paper: Parameters of Monovalent Ions in the Amber-99 Forcefield: Assesment of Inaccuracies and Proposed Improvements http://pubs.acs.org/doi/abs/10.1021/jp0765392 There, they simulate nucleic acids using a combination of Amber and OPLS sigma and epsilon for the ions. I have tried that in the case of my protein, just changing the ion sigma and epsilon in the topology by those corresponding to OPLS, but I still observe aggregation for the ions. Would this combination of Amber and OPLS have any kind of potential problem during the simulation? Has anybody any idea to avoid this type of artefact? Thank you very much in advance, Rebeca. > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] crystals of KCl during simulation > Date: Mon, 1 Jun 2009 14:34:55 +0200 > From: baa...@smplinux.de > > > Hi, > > rega...@hotmail.com said: > >> [..] but after equilibration I have observed that KCl is aggregating, like > >> if it was making crystals. When I used NaCl instead KCl, this not > >> happened. > > >> Does anybody has any idea about the reason of the behaviour of KCl in > >> the simulation? > > This even does happen with Amber :) So my guess is you correctly transferred > the parameters, but stumbled upon an artefact. If you check the recent > literature you may notice that many publications with Amber using K+ > only employ minimal (neutralising) salt conditions as a workaround. At > least this is what we did recently [1]. > > Marc Baaden > > [1] Interactions between neuronal fusion proteins explored by molecular > dynamics, Biophys.J.94, 2008, 3436-3446. > http://dx.doi.org/10.1529/biophysj.107.123117 > > -- > Dr. Marc Baaden - Institut de Biologie Physico-Chimique, Paris > mailto:baa...@smplinux.de - http://www.baaden.ibpc.fr > FAX: +33 15841 5026 - Tel: +33 15841 5176 ou +33 609 843217 > > > ___ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php _ Comparte, crea, disfruta… Descubre todo, en estos vídeos http://www.windowslive.es ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] crystals of KCl during simulation
Hi, I am trying to simulate a protein in aqueous solution 1M (KCl) with Gromacs and using the amber force field. I get the topology of the solvated protein - without the ions- from amber (Leap) and then used the script amb2gmx.pl to obtain the Gromacs .top and .gro files. I did not introduced the ions from Amber because amb2gmx.pl is only written for NaCl, so I used genion to ionize the system. I added the lines correspondent to the ions in Amber to the .top of Gromacs: [ atomtypes ] amber99_51 K 0. 0. A 4.73602e-01 1.37235e-03 ; K+ ion amber99_30Cl 0. 0. A 4.40104e-01 4.18400e-01 ; Cl- ion [ moleculetype ] ; molname nrexcl K 1 [ atoms ] ; nr type resnr residue atom cgnr charge mass 1 amber99_51 1K K 1 1 39.1 [ moleculetype ] ; molname nrexcl Cl 1 [ atoms ] ; nr type resnr residue atom cgnr charge mass 1 amber99_30 1Cl Cl 1 -1 35.45000 and everything went OK, but after equilibration I have observed that KCl is aggregating, like if it was making crystals. When I used NaCl instead KCl, this not happened. Does anybody has any idea about the reason of the behaviour of KCl in the simulation? Thank you very much in advance for your help. Rebeca Garcia Academic Visitor Dep. of Biochemistry University of Oxford _ Descárgate ahora el nuevo Internet Explorer 8 y ten a tu alcance todos los servicios de Windows Live ¡Gratis! http://ie8.msn.com/microsoft/internet-explorer-8/es-es/ie8.aspx___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] bond, angle and dihedral restraints in Gromacs
Thank you very much for the suggestion. Actually, I am trying to reproduce the results from another publication (JACS 2005, 127, 7166) http://pubs.acs.org/doi/full/10.1021/ja050044d where they used Gromacs/amber to simulate a CNT. They apply: "Carbon−carbon bond lengths of 0.14 nm and bond angles of 120° were maintained by harmonic potentials with spring constants of 393 960 kJ mol-1 nm-2 and 527 kJ mol-1 deg-2 before relaxation. In addition, a weak dihedral angle potential was applied to bonded carbon atoms." So, as I understand, they apply RESTRAINTS to the bonds, angles and dihedrals. I have tried to construct the [distance_restraints] for my system (I show you here a little part): [ distance_restraints ] ; atom1 atom2 type index type2 low up1 up2 fac 1 310 1 1 1 0.142 0.146 0.150 1.0 2 290 1 2 1 0.142 0.146 0.150 1.0 3 291 1 3 1 0.142 0.146 0.150 1.0 (...) but I don' t understand very well which value should I write for "low up1 up2". The manual says that "the columns low, up1 and up2 hold the values of r0 , r1 and r2 from eqn. 4.76", but looking at this equation I still don' t understand which should be the better values for my case. I have looked into the mail archive, and some other people asked for that, but I did not find any proper solution. How could I choose the best values for "low up1 up2" to restrain my bond values to 1.42 Amstrong? The other question is about angle restraints, I have found indications in the wiki of how to treat the dihedral restraints (http://wiki.gromacs.org/index.php/Dihedral_Restraints), however I did not find any similar for the angle restraints. I have seen in the mail archive that 2 pairs of atoms should be used, but I did not find anything to trust in. Could you please give me some indications of how to treat angle restraints? Thank you very much, Best wishes, Rebeca Garcia Parc Cientific de Barcelona Spain > Date: Thu, 21 May 2009 12:41:57 -0400 > From: jalem...@vt.edu > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] bond, angle and dihedral restraints in Gromacs > > > > Rebeca García Fandiño wrote: > > Hello, > > I would like to simulate a CNT and I want to apply a harmonic potential: > > -on the C-C bonds > > -on the bond angles > > -on the dihedral angles > > with a different spring constant for each case. > > > > I have read Section 4.3 from Gromacs manual, but I actually have some > > doubts about how to include this in the topology. > > > > -for the distance restraints I have tried to use genrestr: > > > > genrestr -f cnt_wat_gmx_centered.gro -o posre_dist.itp -disre -fc 40 > > > > The file I obtain is something like: > > > > ; distance restraints for UNK of cnt_wat_gmx.gro created by > > rdparm2gmx.pl Wed May 20 10:20:59 BST 2009 > > > > [ distance_restraints ] > > ; i j ? label funct loup1up2 weight > > 1 2 1 0 1 0.403354 0.6033541.60335 1 > > 1 3 1 1 1 0.587676 0.7876761.78768 1 > > 1 4 1 2 1 0.769212 0.9692121.96921 1 > > 1 5 1 3 10.860811.060812.06081 1 > > (...) > > > > This is different from the [distance_restraint] example shown in pag 69 > > of the manual, now I don' t have the fac column. I would like to apply a > > The format of the distance_restraints section appears correct. If you read > the > description of the "fac" column, it is a weighting factor for that particular > restraint. So therefore, "weight" is probably equivalent. > > > spring constant of 40 to C-C bonds, but where is the constant here? > > How could I apply a determined spring constant? In the .mdp file? > > Besides, all the distances are restrained... Is there any way to > > restrain only the C-C bonds? I mean I don' t want to restrain the > > distance between a carbon and a carbon far away from it, only > > restraining the neighbouring carbons to a distance of 1.4 A. > > > > You cannot use genrestr for this purpose. Using genrestr -disre generates a > matrix of all atoms you specify. Also, -fc is expected to be used with > position > restraints; note the format given in genrestr -h. > > Are you really interested in applying restraints to all bonds, angles, > dihedrals, and distances? Realize that constraints (Section 5.5) and > restraints > are separate ideas in Gromacs. > > If you want to define your own force constants for bonds, angles, etc. simply > do
[gmx-users] bond, angle and dihedral restraints in Gromacs
Hello, I would like to simulate a CNT and I want to apply a harmonic potential: -on the C-C bonds -on the bond angles -on the dihedral angles with a different spring constant for each case. I have read Section 4.3 from Gromacs manual, but I actually have some doubts about how to include this in the topology. -for the distance restraints I have tried to use genrestr: genrestr -f cnt_wat_gmx_centered.gro -o posre_dist.itp -disre -fc 40 The file I obtain is something like: ; distance restraints for UNK of cnt_wat_gmx.gro created by rdparm2gmx.pl Wed May 20 10:20:59 BST 2009 [ distance_restraints ] ; i j ? label funct loup1up2 weight 1 2 1 0 1 0.403354 0.6033541.60335 1 1 3 1 1 1 0.587676 0.7876761.78768 1 1 4 1 2 1 0.769212 0.9692121.96921 1 1 5 1 3 10.860811.060812.06081 1 (...) This is different from the [distance_restraint] example shown in pag 69 of the manual, now I don' t have the fac column. I would like to apply a spring constant of 40 to C-C bonds, but where is the constant here? How could I apply a determined spring constant? In the .mdp file? Besides, all the distances are restrained... Is there any way to restrain only the C-C bonds? I mean I don' t want to restrain the distance between a carbon and a carbon far away from it, only restraining the neighbouring carbons to a distance of 1.4 A. Another question is: Is there any tool to construct the equivalent angle_restraints and dihedral_restraints in an authomatic way, or should I do it by hand? Thank you very much in advance for your help. Best wishes, Dr. Rebeca Garcia Parc Cientific de Barcelona Spain _ ¡Quítate unos clics! Ahora, Internet Explorer 8 tiene todo lo que te gusta de Windows Live ¡Consíguelo gratis! http://ie8.msn.com/microsoft/internet-explorer-8/es-es/ie8.aspx___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] identical energies in a rerun calculation
Hello, I am trying to do a -rerun simulation in Gromacs 4.0.4 to calculate the interaction energy between 2 residues using the trajectory I already had from the previous simulation: /gpfs/apps/GROMACS/4.0.4/bin/mdrun -v -deffnm E_interaccion_Asp -dlb auto -rerun equilibrado3_19.xtc I am having very strange results, since the calculation finishes without errors, however, when I look at the .log file I found that all the Energetic terms are just the same for all steps; you can see here a piece of the log file, they are identical for each step: --- Charge group distribution at step 14000: 20243 20228 20307 20264 20218 20237 20184 20187 20125 20139 20268 20231 20251 20134 20223 20180 Step Time Lambda 14000 28.00.0 Energies (kJ/mol) Angle G96AngleProper Dih. Ryckaert-Bell. Improper Dih. 3.06349e+051.40143e+041.04094e+051.39048e+052.14284e+04 LJ-14 Coulomb-14LJ (SR)LJ (LR) Coulomb (SR) 8.86844e+043.07537e+058.73300e+05 -6.98493e+04 -1.05915e+07 Coul. recip. PotentialKinetic En. Total EnergyTemperature -3.83299e+06 -1.26398e+073.11453e+06 -9.52530e+064.64769e+02 Pressure (bar) Cons. rmsd () 1.71651e+040.0e+00 DD step 14999 load imb.: force 3.1% pme mesh/force 0.777 Charge group distribution at step 15000: 20243 20228 20307 20264 20218 20237 20184 20187 20125 20139 20268 20231 20251 20134 20223 20180 Step Time Lambda 15000 30.00.0 Energies (kJ/mol) Angle G96AngleProper Dih. Ryckaert-Bell. Improper Dih. 3.06349e+051.40143e+041.04094e+051.39048e+052.14284e+04 LJ-14 Coulomb-14LJ (SR)LJ (LR) Coulomb (SR) 8.86844e+043.07537e+058.73300e+05 -6.98493e+04 -1.05915e+07 Coul. recip. PotentialKinetic En. Total EnergyTemperature -3.83299e+06 -1.26398e+073.11453e+06 -9.52530e+064.64769e+02 Pressure (bar) Cons. rmsd () 1.71651e+040.0e+00 DD step 15999 load imb.: force 3.3% pme mesh/force 0.792 Charge group distribution at step 16000: 20243 20228 20307 20264 20218 20237 20184 20187 20125 20139 20268 20231 20251 20134 20223 20180 Step Time Lambda --- Could anyone tell me what could be wrong? Thank you very much in advance for your help. Best wishes, Rebeca Garcia Parc Cientific de Barcelona rega...@hotmail.com _ ¿Quieres que tus hijos naveguen seguros? Aprende aquí cómo con Protección Infantil http://www.protegeatushijos.com___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] problem extending simulation 64 proc
Hello, I have a problem in extending a MD simulation in Gromacs. When I use 32 processors for the calculation, everything goes OK. The simulation finishes well and I can extend it with tpbconv. However, I would like to increase the number of processors used up to 64. Using the same options for mdrun as I have used for 32 proc except for the number of processors: srun -n 64 /gpfs/apps/GROMACS/4.0.2/bin/mdrun -v -deffnm equilibrado9 -dlb auto I get this error: --- Program mdrun, VERSION 4.0.2 Source code file: domdec_setup.c, line: 132 Fatal error: Could not find an appropriate number of separate PME nodes. i.e. >= 0.474960*#nodes (58) and <= #nodes/2 (64) and reasonable performance wise (grid_x=384, grid_y=162). Use the -npme option of mdrun or change the number of processors or the PME grid dimensions, see the manual for details. When I changed to srun -n 64 /gpfs/apps/GROMACS/4.0.2/bin/mdrun -v -deffnm equilibrado9 -dlb auto –npme 32 the calculation finished correctly. However, when I try to extend this simulation with tpbconv: /gpfs/apps/GROMACS/4.0.4/bin/tpbconv -s equilibrado9.tpr -f equilibrado9.trr -e equilibrado9.edr -n index.ndx -o equilibrado10.tpr -extend 1600 The process dies, I don´t know why: READING COORDS, VELS AND BOX FROM TRAJECTORY equilibrado9.trr... Opened equilibrado9.edr as single precision energy file trn version: GMX_trn_file (single precision) Readtrr frame452: step 2652000 time 5304.000Killed When I used gmxcheck I have not found anything strange. I have also tried with the version 4.0.4 of Gromacs to do tpbconv, but the error is the same. This occurred in several calculations, always using 64 processors and -npme 32, so it is not a punctual error, something must be happening in the calculation but I don´t know what. Does anybody has any idea? Thank you very much for your help in advance, Rebeca Garcia Parc Cientific of Barcelona rega...@hotmail.com _ Nuevo Windows Live, un mundo lleno de posibilidades. Descúbrelo. http://www.microsoft.com/windows/windowslive/default.aspx___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] problem with variable fio in REMD
Hello, I am trying to do Replica Exchange with 50 replicas, but I am having problems when using trjcat with -demux. trjcat -f mdA_0.xtc mdA_1.xtc mdA_2.xtc mdA_3.xtc mdA_4.xtc mdA_5.xtc mdA_6.xtc mdA_7.xtc mdA_8.xtc mdA_9.xtc mdA_10.xtc mdA_11.xtc mdA_12.xtc mdA_13.xtc mdA_14.xtc mdA_15.xtc mdA_16.xtc mdA_17.xtc mdA_18.xtc mdA_19.xtc mdA_20.xtc mdA_21.xtc mdA_22.xtc mdA_23.xtc mdA_24.xtc mdA_25.xtc mdA_26.xtc mdA_27.xtc mdA_28.xtc mdA_29.xtc mdA_30.xtc mdA_31.xtc mdA_32.xtc mdA_33.xtc mdA_34.xtc mdA_35.xtc mdA_36.xtc mdA_37.xtc mdA_38.xtc mdA_39.xtc mdA_40.xtc mdA_41.xtc mdA_42.xtc mdA_43.xtc mdA_44.xtc mdA_45.xtc mdA_46.xtc mdA_47.xtc mdA_48.xtc mdA_49.xtc -o trajout_A.xtc -demux replica_index.xvg I get the replica_index.xvg from demux.pl mdA_0.log. The calculation finishes with this error: Read 50 sets of 500 points, dt = 2 Reading frame 300 time 12.000 --- Program trjcat, VERSION 3.3.99_development_20080718 Source code file: gmxfio.c, line: 822 Range checking error: Variable fio has value 268369076. It should have been within [ 0 .. 51 ] ---I have found an error analogous to this in the mail archive (http://www.mail-archive.com/gmx-users@gromacs.org/msg18278.html), but it is unresolved.Please, could anyone help me?Thank you very much, Rebeca GarcíaParc Cientific de barcelonarega...@hotmail.com _ Consigue gratis el nuevo Messenger. ¡Descárgatelo! http://download.live.com/___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] problem with variable fio in REMD
Hello, I am trying to do Replica Exchange with 50 replicas, but I am having problems when using trjcat with -demux. trjcat -f mdA_0.xtc mdA_1.xtc mdA_2.xtc mdA_3.xtc mdA_4.xtc mdA_5.xtc mdA_6.xtc mdA_7.xtc mdA_8.xtc mdA_9.xtc mdA_10.xtc mdA_11.xtc mdA_12.xtc mdA_13.xtc mdA_14.xtc mdA_15.xtc mdA_16.xtc mdA_17.xtc mdA_18.xtc mdA_19.xtc mdA_20.xtc mdA_21.xtc mdA_22.xtc mdA_23.xtc mdA_24.xtc mdA_25.xtc mdA_26.xtc mdA_27.xtc mdA_28.xtc mdA_29.xtc mdA_30.xtc mdA_31.xtc mdA_32.xtc mdA_33.xtc mdA_34.xtc mdA_35.xtc mdA_36.xtc mdA_37.xtc mdA_38.xtc mdA_39.xtc mdA_40.xtc mdA_41.xtc mdA_42.xtc mdA_43.xtc mdA_44.xtc mdA_45.xtc mdA_46.xtc mdA_47.xtc mdA_48.xtc mdA_49.xtc -o trajout_A.xtc -demux replica_index.xvg I get the replica_index.xvg from demux.pl mdA_0.log. The calculation finishes with this error: Read 50 sets of 500 points, dt = 2 Reading frame 300 time 12.000 --- Program trjcat, VERSION 3.3.99_development_20080718 Source code file: gmxfio.c, line: 822 Range checking error: Variable fio has value 268369076. It should have been within [ 0 .. 51 ] ---I have found an error analogous to this in the mail archive (http://www.mail-archive.com/gmx-users@gromacs.org/msg18278.html), but it is unresolved.Please, could anyone help me?Thank you very much, Rebeca GarcíaParc Cientific de barcelonarega...@hotmail.com _ Consigue gratis el nuevo Messenger. ¡Descárgatelo! http://download.live.com/___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Magic Number Error in XTC file
Hello, I am trying to joing different .xtc fragments of a gromacs trajectory using trjcat (Gromacs 4.0.2 version). trjcat_sp -f file1.xtc file2.xtc -o join1_2.xtc I get the following error: (...) Reading frame 1 time 22202.002Summary of files and start times used: FileStart time Time step-file1.xtc 0.000 ps 2.000 psfile2.xtc22200.002 ps2.000 psReading frame 0 time0.000Continue writing frames from file1.xtc t=0 ps, frame=0 -> frame 5610 time 11220.001 ps -> frame 5000 time 1.000 ps---Program trjcat_sp, VERSION 4.0.2Source code file: xtcio.c, line: 85Fatal error:Magic Number Error in XTC file (read 0, should be 1995)--- Please, could anyone help me with the origin of this error? Thank you very much for your help, in advance. Best wishes, Rebeca Garcia Parc Cientific de Barcelona rega...@hotmail.com _ Descubre cómo compartir tus fotos con Windows Live. ¡Pruébalo ya! http://home.live.com/___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] help with REMD
Hello, I am trying to do REMD for a protein unfolding. I am following the information given in http://wiki.gromacs.org/index.php/REMD but I am completely new in these type of simulations. I would like to ask two questions to more advanced users. I hope you could help me: -I have seen that the exchange rate should be typically between 0.2 and 0.3. Where can I extract the exchange rate from my outputs? For example in the output below the exchange rate would be "Repl pr .08 .00 .13"? Should I calculate a mean for all exchanges and all replicas and check if this mean is between 0.2 and 0.3?Repl 0 <-> 1 dE = 2.492e+00Repl ex 012 345Repl pr .08 .00 .13Replica exchange at step 2000 time 4Repl ex 0123 x 45Repl pr.00 1.0 -Another question is about restarting simulations. I have though doing it with tpbconv and then concatenate the .log files to use demux.pl. Is this correct? Thank you very much for your help. Best wishes, Rebeca Garcia Parc Cientific of Barcelona Barcelona University rega...@hotmail.com _ ¿Quieres ver los mejores videos de MSN? Enciende Messenger TV http://messengertv.msn.com/mkt/es-es/default.htm ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] Urea topology problem
OK, including a mass colum, as Justin A. Lemkul suggested, worked well. Now grompp does not give errors. Why should I not use this model for urea? I have found also another model in the contributions section, for a urea/water box 10M, but why should I trust more in a user contribution than in a *itp included in Gromacs? I don´t have much experience with Gromacs, so any coment will be wellcome. Thank you very much for your help and suggestions. Best wishes, Rebeca García Parc Cientific de Barcelona rega...@hotmail.com> Date: Thu, 18 Dec 2008 19:50:03 +0100> From: sp...@xray.bmc.uu.se> To: gmx-users@gromacs.org> Subject: Re: [gmx-users] Urea topology problem> > Rebeca García Fandiño wrote:> > Hello,> > I don´t understand the correction I should do from itp.> > I have removed from the urea original urea.itp these lines,> > don't use this model. do a proper literature search.> > > > > #ifdef Boek> > 1 C 1 UREA C1 1 0.38> > 2 O 1 UREA O2 1 -0.38> > 3 NT 1 UREA N3 2 -0.83> > 4 H 1 UREA H4 2 0.415> > 5 H 1 UREA H5 2 0.415> > 6 NT 1 UREA N6 3 -0.83> > 7 H 1 UREA H7 3 0.415> > 8 H 1 UREA H8 3 0.415> > #else> > #endif[ moleculetype ]> > > > so now, my urea.itp file is:> > > > ; name nrexcl> > Urea 3> > [ atoms ]> > ; nr type resnr residu atom cgnr charge> > 1 C 1 UREA C1 1 0.683> > 2 O 1 UREA O2 1 -0.683> > 3 NT 1 UREA N3 2 -0.622> > 4 H 1 UREA H4 2 0.346> > 5 H 1 UREA H5 2 0.276> > 6 NT 1 UREA N6 3 -0.622> > 7 H 1 UREA H7 3 0.346> > 8 H 1 UREA H8 3 0.276> > [ bonds ]> > ; ai aj funct b0 kb> > 3 4 1 1.00e-01 3.744680e+05> > 3 5 1 1.00e-01 3.744680e+05> > 6 7 1 1.00e-01 3.744680e+05> > 6 8 1 1.00e-01 3.744680e+05> > 1 2 1 1.23e-01 5.020800e+05> > 1 3 1 1.33e-01 3.765600e+05> > 1 6 1 1.33e-01 3.765600e+05> > [ pairs ]> > ; ai aj funct c6 c12> > 2 4 1 0.00e+00 0.00e+00> > 2 5 1 0.00e+00 0.00e+00> > 2 7 1 0.00e+00 0.00e+00> > 2 8 1 0.00e+00 0.00e+00> > 3 7 1 0.00e+00 0.00e+00> > 3 8 1 0.00e+00 0.00e+00> > 4 6 1 0.00e+00 0.00e+00> > 5 6 1 0.00e+00 0.00e+00> > [ angles ]> > ; ai aj ak funct th0 cth> > 1 3 4 1 1.20e+02 2.928800e+02> > 1 3 5 1 1.20e+02 2.928800e+022 1 6 1 1.215000e+02 5.020800e+02> > 3 1 6 1 1.17e+02 5.020800e+02> > [ dihedrals ]> > ; ai aj ak al funct phi cp mult> > 2 1 3 4 1 1.80e+02 3.347200e+01 2.00e+00> > 6 1 3 4 1 1.80e+02 3.347200e+01 2.00e+00> > 2 1 3 5 1 1.80e+02 3.347200e+01 2.00e+00> > 6 1 3 5 1 1.80e+02 3.347200e+01 2.00e+00> > 2 1 6 7 1 1.80e+02 3.347200e+01 2.00e+00> > 3 1 6 7 1 1.80e+02 3.347200e+01 2.00e+00> > 2 1 6 8 1 1.80e+02 3.347200e+01 2.00e+00> > 3 1 6 8 1 1.80e+02 3.347200e+01 2.00e+00> > [ dihedrals ]> > ; ai aj ak al funct q0 cq> > 3 4 5 1 2 0.00e+00 1.673600e+02> > 6 7 8 1 2 0.00e+00 1.673600e+02> > 1 3 6 2 2 0.00e+00 1.673600e+02> > > > 4 3 5 1 1.20e+02 3.347200e+02> > 1 6 7 1 1.20e+02 2.928800e+02> > 1 6 8 1 1.20e+02 2.928800e+02> > 7 6 8 1 1.20e+02 3.347200e+02> > 2 1 3 1 1.215000e+02 5.020800e+02> > > > > > Following Chapter 5 in the manual (page 102), the file described for > > urea.itp is the same as mine. For the topology (page 103)> > #include "ffgmx.itp" is used, but I don´t see any more different.> > With this modification in the urea.itp I get the same error. Any idea of > > what could be the problem?> > Thank you very much for your help,> > > > Rebeca Garcia > > Parc Cientific de Barcelona> > rega...@hotmail.com <mailto:rega...@hotmail.com>> > > > > > > > > > > > > Date: Thu, 18 Dec 2008 09:21:41 -0500> > > From: jalem...@vt.edu> > > To: gmx-users@gromacs.org> > > Subject: Re: [gmx-users] Urea topology problem> > >> > >> > >> > > Rebeca García Fandiño wrote:> > >> > > > > >> > > >> > > > ERROR 1 [file solvated.top, line 39]:> > > >> > > > atom C1 (Res UREA-1) has mass 0> > > >> > > >> > >> > > In urea.itp, no masses are defined. If you correct the format of this > > file (see> > > Chapter 5 of the manual), then this issue should be resolved.> > >> > >> > > >> > > > Which force field does
RE: [gmx-users] Urea topology problem
Hello, I don´t understand the correction I should do from itp. I have removed from the urea original urea.itp these lines, #ifdef Boek 1 C 1UREA C1 1 0.38 2 O 1UREA O2 1 -0.38 3 NT 1UREA N3 2 -0.83 4 H 1UREA H4 2 0.415 5 H 1UREA H5 2 0.415 6 NT 1UREA N6 3 -0.83 7 H 1UREA H7 3 0.415 8 H 1UREA H8 3 0.415#else #endif[ moleculetype ] so now, my urea.itp file is: ; name nrexclUrea 3 [ atoms ]; nr type resnr residu atom cgnr charge1 C 1 UREA C1 1 0.6832 O 1 UREA O2 1 -0.6833 NT 1 UREA N3 2 -0.6224 H 1 UREA H4 2 0.3465 H 1 UREA H5 2 0.2766 NT 1 UREA N6 3 -0.6227 H 1 UREA H7 3 0.3468 H 1 UREA H8 3 0.276 [ bonds ]; ai aj funct b0 kb3 4 1 1.00e-01 3.744680e+053 5 1 1.00e-01 3.744680e+056 7 1 1.00e-01 3.744680e+056 8 1 1.00e-01 3.744680e+051 2 1 1.23e-01 5.020800e+051 3 1 1.33e-01 3.765600e+051 6 1 1.33e-01 3.765600e+05 [ pairs ]; ai aj funct c6 c122 4 1 0.00e+00 0.00e+002 5 1 0.00e+00 0.00e+002 7 1 0.00e+00 0.00e+002 8 1 0.00e+00 0.00e+003 7 1 0.00e+00 0.00e+003 8 1 0.00e+00 0.00e+004 6 1 0.00e+00 0.00e+005 6 1 0.00e+00 0.00e+00 [ angles ]; ai aj ak funct th0 cth1 3 4 1 1.20e+02 2.928800e+021 3 5 1 1.20e+02 2.928800e+022 1 6 1 1.215000e+02 5.020800e+023 1 6 1 1.17e+02 5.020800e+02 [ dihedrals ]; ai aj ak al funct phi cp mult 2 1 3 4 1 1.80e+02 3.347200e+01 2.00e+006 1 3 4 1 1.80e+02 3.347200e+01 2.00e+002 1 3 5 1 1.80e+02 3.347200e+01 2.00e+006 1 3 5 1 1.80e+02 3.347200e+01 2.00e+002 1 6 7 1 1.80e+02 3.347200e+01 2.00e+003 1 6 7 1 1.80e+02 3.347200e+01 2.00e+002 1 6 8 1 1.80e+02 3.347200e+01 2.00e+003 1 6 8 1 1.80e+02 3.347200e+01 2.00e+00 [ dihedrals ]; ai aj ak al funct q0 cq3 4 5 1 2 0.00e+00 1.673600e+026 7 8 1 2 0.00e+00 1.673600e+021 3 6 2 2 0.00e+00 1.673600e+024 3 5 1 1.20e+02 3.347200e+021 6 7 1 1.20e+02 2.928800e+021 6 8 1 1.20e+02 2.928800e+027 6 8 1 1.20e+02 3.347200e+022 1 3 1 1.215000e+02 5.020800e+02 Following Chapter 5 in the manual (page 102), the file described for urea.itp is the same as mine. For the topology (page 103) #include "ffgmx.itp" is used, but I don´t see any more different. With this modification in the urea.itp I get the same error. Any idea of what could be the problem? Thank you very much for your help, Rebeca Garcia Parc Cientific de Barcelona rega...@hotmail.com > Date: Thu, 18 Dec 2008 09:21:41 -0500> From: jalem...@vt.edu> To: > gmx-users@gromacs.org> Subject: Re: [gmx-users] Urea topology problem> > > > > Rebeca García Fandiño wrote:> > > > > > > ERROR 1 [file solvated.top, > line 39]:> > > > atom C1 (Res UREA-1) has mass 0> > > > > > In urea.itp, no > masses are defined. If you correct the format of this file (see > Chapter 5 > of the manual), then this issue should be resolved.> > > > > > Which force > field does this urea.itp correspond to? Where should it look > > for the > atomtypes of urea?> > > >> > The .atp file corresponding to the force field > you are using (ffG43a2). The > atomtypes for urea appear to be generic for > use with the Gromos96 force fields. > There are specific atomtypes within > ffG53a6 for urea, if you want to use the > newer force field (check the > ffG53a6.rtp file for the urea parameters).> > -Justin> > > > > > Thank you > very much for your help,> > > > > > > > Rebeca Garcia> > > > Parc Cientific > de Barcelona> > > > rega...@hotmail.com> > > > > > > > > > ¿Aún no tienes Internet Explorer 7? Bájatelo y consigue un regalo gratis > > > <http://vivelive.com/ieak7/>> > > > > > > > > > > > ___> > gmx-users mailing list > gmx-users@gromacs.org> > http://www.gromacs.org/mailman/listinfo/gmx-users> > > Please search the archive at http://www.gromacs.org/search before posting!> > > Please don't post (un)subscribe requests to the list. Use the > > www > interface or send it to gmx-users-requ...@gromacs.org.> > Can't post? Read > http://www.gromacs.org/mailing_lists/users.php> > -- > > > > Justin A. Lemkul> Graduate
[gmx-users] Urea topology problem
Hello, I would like to simulate a proteína in urea, using Gromacs. I have tried to use the box included in Gromacs by default (urea+h2o.gro and urea.itp). The topology of the urea/water-solvated protein is: ; Include forcefield parameters #include "ffG43a2.itp" #include "protein.itp" ; Include Position restraint file #ifdef POSRES #include "posre.itp" #endif ; Include water and urea topology #include "urea.itp" #include "spc.itp" #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif [ system ] ; Name Protein in water/urea [ molecules ] ; Compound#mols Protein 1 UREA426 SOL 5885 When I try grompp -f min.mdp -c solvated_urea.gro -p solvated.top -o min.tpr I get these errors: ERROR 1 [file solvated.top, line 39]: atom C1 (Res UREA-1) has mass 0 ERROR 2 [file solvated.top, line 39]: atom O2 (Res UREA-1) has mass 0 ERROR 3 [file solvated.top, line 39]: atom N3 (Res UREA-1) has mass 0 ERROR 4 [file solvated.top, line 39]: atom H4 (Res UREA-1) has mass 0 ERROR 5 [file solvated.top, line 39]: atom H5 (Res UREA-1) has mass 0 ERROR 6 [file solvated.top, line 39]: atom N6 (Res UREA-1) has mass 0 ERROR 7 [file solvated.top, line 39]: atom H7 (Res UREA-1) has mass 0 ERROR 8 [file solvated.top, line 39]: atom H8 (Res UREA-1) has mass 0 Which force field does this urea.itp correspond to? Where should it look for the atomtypes of urea? Thank you very much for your help, Rebeca Garcia Parc Cientific de Barcelona rega...@hotmail.com _ ¡Accede al correo desde el móvil! ¿Qué opinas? http://vivelive.com/encuesta/___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] area per lipid in ondulated membranes
Hello, I am trying to calculate the area per lipid for a quite big membrane formed by a unique type o lipid (DOPC). I can see ondulations in the membrane, so I am not sure of the right area I should have to employ, because the max and min values in x and y axes are not representative for the real area of each layer. Could anybody suggest how could I calculate this paremeter in this type of simulations? Thank you very much in advance. Rebeca García Fandiño Parc Cientific de Barcelona [EMAIL PROTECTED] _ Prueba los prototipos de los últimos en MSN Motor http://motor.es.msn.com/___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] problems with PBC in editconf
Hello, I would like to transform to pdb a .gro file I have obtained from an equilibration in Gromacs. I have tried directly with editconf: editconf -f equilibrated.gro -o equilibrated.pdb but the lipids of my membrane appear divided due to PBC. Then I have tried: editconf -f equilibrated.gro -o equilibrated.pdb -pbc and they don´t divide, but the membrane and protein are in a side and the water and ions in the other side. They are not where they should be. How could I convert a .gro file to a .pdb with no PBC and in the right place, like the output file of a NAMD or AMBER program? Thank you very much for your help in advance, Rebeca García Fandiño Parc Cientific of Barcelona _ ¿Preparándote para el verano? En Windows Live Search encontrarás las mejores dietas para conseguir tu peso ideal http://search.live.com/results.aspx?q=dieta&form=MKTPG___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] invalid number of nodes
Thanks a lot for your suggestion. What I was refering was to this post: http://www.gromacs.org/pipermail/gmx-developers/2008-February/002378.html "OR use the 3.3 grompp to produce the mdp files since it will automatically set the fourier grid to fit the number of processors." Sorry for not explaining it better. Anyway, in the new version of Gromacs, the -np option of grompp does not work, does it? I am new in Gromacs, and I am using a version installed in a common cluster. I don´t know if I could install your modificated version myself. If I use grompp from the my new version, and I only change fourier_nx and fourier_ny in the input .mdp file, would it be enough to create a correct mdp.out file that works. Best wishes, Rebeca García Fandiño Parc Cientific de Barcelona From: [EMAIL PROTECTED]: [EMAIL PROTECTED]: RE: [gmx-users] invalid number of nodesDate: Wed, 13 Aug 2008 14:52:30 +0200 Hi,I don't understand your remark about the mdp file.Where on the wiki does it say something like this?The number of processors is never present in the mdp file.Just use the new version of grompp.A week ago I have committed large changes to the CVSwhich make the tpr files much smaller and large simulations a bit more efficient.Berk. From: [EMAIL PROTECTED]: [EMAIL PROTECTED]: Wed, 13 Aug 2008 11:51:56 +Subject: [gmx-users] invalid number of nodes Hello, I want to simulate a membrane+proteína system (more than 700.000 atoms) with Gromacs 4 and I would like to use 512 proc. I am creating the mdp file with Gromacs 3, since I have read in the wiki that it was a good way to include the number or processors ins the mdp file for the new version. For grompp with Gromacs 3.3 I amincluding this options in the input mdp file: fourierspacing = 0.12 fourier_nx = 1024 fourier_ny = 1024 fourier_nz = 0 but when I execute: grompp -f equilibrado2.mdp -c equilibrado.gro -p para_equilibrado.top -o equilibrado2.tpr -n index.ndx -np 512 I receive this error: --- Program grompp, VERSION 3.3.3 Source code file: grompp.c, line: 1021 Fatal error: invalid number of nodes 512 --- When I had tried the same with 256 proc, using fourier_nx= fourier_ny=512, the correspondent error did not appear. Is there a limit of processors in Gromacs for grompp or which could be the problem? Thank you very much for your help in advance, Rebeca García Fandiño Parc Cientific of Barcelona ¿Todavía no conoces El Duelo? Descúbrelo y reta a tus contactos de Messenger El Duelo Express yourself instantly with MSN Messenger! MSN Messenger _ ¿Quieres los emoticonos y guiños más divertidos? Descárgate Internet Explorer 7, y consigue contenidos exclusivos cada semana. ¡Gratis! http://www.vivelive.com/IEAK7___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] invalid number of nodes
Hello, I want to simulate a membrane+proteína system (more than 700.000 atoms) with Gromacs 4 and I would like to use 512 proc. I am creating the mdp file with Gromacs 3, since I have read in the wiki that it was a good way to include the number or processors ins the mdp file for the new version. For grompp with Gromacs 3.3 I amincluding this options in the input mdp file: fourierspacing = 0.12 fourier_nx = 1024 fourier_ny = 1024 fourier_nz = 0 but when I execute: grompp -f equilibrado2.mdp -c equilibrado.gro -p para_equilibrado.top -o equilibrado2.tpr -n index.ndx -np 512 I receive this error: --- Program grompp, VERSION 3.3.3 Source code file: grompp.c, line: 1021 Fatal error: invalid number of nodes 512 --- When I had tried the same with 256 proc, using fourier_nx= fourier_ny=512, the correspondent error did not appear. Is there a limit of processors in Gromacs for grompp or which could be the problem? Thank you very much for your help in advance, Rebeca García Fandiño Parc Cientific of Barcelona _ ¿Quieres los emoticonos y guiños más divertidos? Descárgate Internet Explorer 7, y consigue contenidos exclusivos cada semana. ¡Gratis! http://www.vivelive.com/IEAK7___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Problems extending a calculation (in steps and Benchmark)
Hello, I am doing a simulation of a membrane + protein using ffG53a6 in Gromacs. First I equilibrated at constant volume and then I changed to semi-isotropic pressure. This is my mdp file: title = EQUILIBRADO cpp = /usr/bin/cpp include = -I../top define = constraints = all-bonds integrator = md dt = 0.002 nsteps = 10 nstxout = 1000 nstvout = 1000 nstlog = 1000 nstenergy = 1000 nstxtcout = 1000 nstlist = 10 ns_type = grid rlist = 1.0 coulombtype = PME rcoulomb= 1.0 vdwtype = cut-off rvdw= 1.4 pme_order = 4 ewald_rtol = 1e-5 optimize_fft= yes ;Berendsen temperature coupling is on Tcoupl = berendsen tau_t = 0.1 0.10.1 tc-grps = Protein DOPC SOL_NA+_CL- ref_t = 310 310310 ; Pressure coupling Pcoupl = Parrinello-Rahman Pcoupltype = Semiisotropic ; Time constant (ps), compressibility (1/bar) and reference P (bar) tau-p= 1.0 1.0 compressibility = 4.6E-5 4.6E-5 ref-p= 1.0 1.0 ;Generate velocities is on at 310 K gen_vel = yes gen_temp= 310 gen_seed= 173529 W hen I did grompp -f equilibrado3.mdp -c equilibrado2.gro -p ionized_system.top -o equilibrado3.tpr -n index.ndx mdrun -v -deffnm equilibrado3 I got a Benchmark of : NODE (s) Real (s) (%) Time: 38960.000 38960.000100.0 10h49:20 (Mnbf/s) (GFlops) (ns/day) (hour/ns) Performance: 93.815 25.746 0.444 54.111 (My system is very big, so the Benchmark is reasonable) The next I did was extending the calculation: tpbconv -s equilibrado3.tpr -f equilibrado3.trr -e equilibrado3.edr -n index.ndx -o equilibrado4.tpr -extend 20 Surpringsingly, the calculation reached 504.722 steps (it should have stopped at 300.000 since I had done 100.000 and extended to 200.000 more!) and if I look at the benchmark I see: NODE (s) Real (s) (%) Time: 172782.000 172782.000100.0 1d23h59:42 (Mnbf/s) (GFlops) (ns/day) (hour/ns) Performance: 85.694 23.514100.010 0.240 What is obviously incorrect. Anybody knows what could be happening? Thank you very much in advance, Rebeca García Fandiño Parc Cientific of Barcelona _ ¿Preparándote para el verano? En Windows Live Search encontrarás las mejores dietas para conseguir tu peso ideal http://search.live.com/results.aspx?q=dieta&form=MKTPG___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] error: 1 particles communicated to PME node 3 (...)
Hello, I am trying to equilibrate a protein+membrane system in Gromacs 4. The minimization went OK, but in the equilibration at constant pressure I got this error: Fatal error:1 particles communicated to PME node 3 are more than a cell length out of the domain decomposition cell of their charge group--- "O My God, They Killed Kenny !" (South Park) Error on node 15, will try to stop all the nodesHalting parallel program mdrun_mpi on CPU 15 out of 32 gcq#254: "O My God, They Killed Kenny !" (South Park) [15] MPI Abort by user Aborting program !mx_finalize() called while some endpoints are still open.MX:s23c2b13:mx_finalize:error 20(errno=2):Busysrun: error: s23c2b13: task15: Exited with exit code 1MX:s23c2b06:Remote endpoint is closed, peer=00:60:dd:48:46:62 (s23c2b13:0)srun: error: s23c2b06: task11: Exited with exit code 1srun: error: s23c2b13: task[12-14]: Killedsrun: Job Failed The calculations stops after 2000 steps: Step Time Lambda 20004.0 0.0 Energies (kJ/mol) Angle Ryckaert-Bell. LJ-14 Coulomb-14LJ (SR)6.17238e+054.06472e+051.89810e+05 5.82538e+053.71263e+06LJ (LR) Coulomb (SR) Coul. recip. Position Rest. Potential -5.12910e+04 -9.09326e+06 -1.97121e+06 1.69698e+06 -3.91010e+06Kinetic En. Total EnergyTemperature Pressure (bar) Cons. rmsd ()2.12885e+06 -1.78125e+063.56627e+02 -2.35301e+042.99204e-05 As input I use: title = EQUILIBRADOcpp = /usr/bin/cppinclude = -I../topdefine = -DPOSRES_D -DPOSRES_Pconstraints = all-bondsintegrator = mddt = 0.002nsteps = 1nstxout = 1000nstvout = 1000nstlog = 1000nstenergy = 1000nstxtcout = 1000nstlist = 10ns_type = gridrlist = 1.0coulombtype = PMErcoulomb= 1.0vdwtype = cut-offrvdw= 1.4pme_order = 4ewald_rtol = 1e-5optimize_fft= yes;Berendsen temperature coupling is onTcoupl = berendsentau_t = 0.1 0.10.1tc-grps = Protein dop SOL_Na_Clref_t = 310 310310; Pressure couplingPcoupl = Parrinello-RahmanPcoupltype = Semiisotropic; Time constant (ps), compressibility (1/bar) and reference P (bar)tau-p = 1.0 1.0compressibility = 4.6E-5 4.6E-5ref-p = 1.0 1.0;Generate velocities is on at 310 Kgen_vel = yesgen_temp = 310gen_seed= 173529 Does anybody which could be the problem? Thank you very much for your help. Best wishes, Rebeca Garcia Fandiño Parc Cientific de Barcelona _ ¿Preparándote para el verano? En Windows Live Search encontrarás las mejores dietas para conseguir tu peso ideal http://search.live.com/results.aspx?q=dieta&form=MKTPG___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] gmx does not recognize HIE as protein
Hello, I am trying to simulate a protein that has 2 chains (in a membrane, but the problem is in the protein). One of the chains of the protein has 416 residues and the other 421. I want to simulate it using the amber force field, so I have prepared the topology for each one of them and then converted them with amb2gmx.pl. When I do grompp of the complete system I can see that it is only considering 821 residues of the protein, and they should be 837!!: Opening library file /gpfs/projects/ub51/ub51077/GROMACS-4.0-DEV/share/gromacs/top/aminoacids.datThere are: 157455 OTHER residuesThere are: 821PROTEIN residuesThere are: 0DNA residues The problem is that the program considers residues HIE out of the protein (histidines): 0 System : 716705 atoms 1 Protein : 12658 atoms 2 Protein-H : 6344 atoms 3 C-alpha : 821 atoms 4 Backbone: 2463 atoms 5 MainChain : 3286 atoms 6 MainChain+Cb: 4038 atoms 7 MainChain+H : 4072 atoms 8 SideChain : 8586 atoms 9 SideChain-H : 3058 atoms 10 Prot-Masses : 12658 atoms 11 Non-Protein : 704047 atoms 12 HIE : 272 atoms 13 dop : 238464 atoms 14 SOL : 464400 atoms 15 Na : 467 atoms 16 Cl : 444 atoms 17 Other : 704047 atoms I have tried to use both chains together and repeating the same, but the result is the same. What could I do? Anybody knows why there is a problem with HIE? Thank you very much in advance, Rebeca Garcia Fandiño Parc Cientific de Barcelona _ ¿Preparándote para el verano? En Windows Live Search encontrarás las mejores dietas para conseguir tu peso ideal http://search.live.com/results.aspx?q=dieta&form=MKTPG___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] membrane with OPLS force field
Ok, thank you very much. However, with this combination I am not using all atoms for the lipds, if I am right and my intention was using all atoms both for the protein and the membrane. Thank you very much for your help. Best wishes, Rebeca García.> Date: Tue, 5 Aug 2008 09:44:17 -0400> From: [EMAIL PROTECTED]> To: gmx-users@gromacs.org> Subject: [gmx-users] membrane with OPLS force field> > There is no such thing as an OPLS bilayer. The method that was specified to combine the opls-PROTEIN and berger-LIPIDS is currently the only way that one can do this combination exactly. What this means, is that if you simulate a bilayer using the files downloaded from Peter Tieleman's website then you get exactly the same thing as when you use the mentioned combination rules for "OPLS" (in cases where you do not have a protein). For the proof, see here:> > http://www.pomeslab.com/files/lipidCombinationRules.pdf> > (although our server appears to be down right now, you might check back near the end of the day today).> > Once you add a protein, however, everything is expected to change, and it has in fact not yet been proven that this combination is without bias. In fact, it will certainly have some bias! However, given the available options I believe that this is currently the best available combination. If the charmm parameters were included in the standard gromacs distribution and somebody else had already tested the lipid properties of that distribution, then I might change my mind. > > Chris.> > -- original message --> > Rebeca García Fandiño wrote:> > > > Hello,> > > I would like to simulate a membrane + protein system using the OPLS > > > force field for both, the protein and the membrane. I have looked for a > > > previous equilibrated membrane simulated using the OPLS force field, but > > > I did not find it.> > > Please, does anybody knows where I could find a membrane simulated with > > > the OPLS force field?> > > > I've never seen one either. The Berger parameters (commonly used) are based in > part on OPLS parameters, and as such, Chris Neale has posted a nice procedure > for modifying the Berger parameters (present at Tieleman's site as lipid.itp) > such that they can be used in conjunction with an OPLS representation of your > protein:> > http://www.gromacs.org/pipermail/gmx-users/2006-May/021416.html> > Recent literature (from Tieleman's group) has suggested that this is a more > accurate representation of protein-lipid interactions than the classic > Gromos+Berger representation that is quite common in the literature.> > If you're desperate for an OPLS bilayer, you may have to generate it yourself.> > ___> gmx-users mailing list gmx-users@gromacs.org> http://www.gromacs.org/mailman/listinfo/gmx-users> Please search the archive at http://www.gromacs.org/search before posting!> Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED]> Can't post? Read http://www.gromacs.org/mailing_lists/users.php _ ¡Lo mejor de MSN y Windows Live en tu móvil! Hotmail, Messenger, Spaces… Pruébalo ya y disfruta de todas sus ventajas donde quieras http://serviciosmoviles.es.msn.com/___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] membrane with OPLS force field
Hello, I would like to simulate a membrane + protein system using the OPLS force field for both, the protein and the membrane. I have looked for a previous equilibrated membrane simulated using the OPLS force field, but I did not find it. Please, does anybody knows where I could find a membrane simulated with the OPLS force field? Thank you very much for your help. Best wishes, Rebeca García Parc Cientific de Barcelona [EMAIL PROTECTED] _ Nuevo Canal Messenger http://www.vivelive.com/ilovemessenger/___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] amb2gmx for big systems
Hello, I am trying to translate the amber topology for a system membrane+protein (dry) to Gromacs. In view of the problems caused in amb2gmx.pl due to the size of the system (more than 600.000 atoms) I had tried another alternative: I created the amber topology for the protein and for a unique lipid molecule separately and I converted them to gromacs using amb2gmx.pl (now, no problems were found, as is logic). Then, from the gromacs topologies, I construct the .itp files for the protein and lipid, removing the correspondent lines and putting them into another file that I have called amberff.itp However, several atomtypes for the lipid are the same than those for the protein, and they have nothing to do between them: [ atomtypes ];name bond_typemasscharge ptype sigma epsilonO O 0. 0. A 2.95992e-01 8.78640e-01H1 H1 0. 0. A 2.64953e-01 6.56888e-02N3N3 0. 0. A 3.25000e-01 7.11280e-01O2O2 0. 0. A 2.95992e-01 8.78640e-01HAHA 0. 0. A 2.64953e-01 6.56888e-02HCHC 0. 0. A 2.64953e-01 6.56888e-02C C 0. 0. A 3.39967e-01 3.59824e-01CT CT 0. 0. A 3.39967e-01 4.57730e-01HPHP 0. 0. A 2.64953e-01 6.56888e-02 and I am getting errors in grompp due to this fact. Does anybody has any idea to solve this? Thank you very much for your help in advance. Rebeca García Fandiño Parc Cientific de Barcelona [EMAIL PROTECTED] _ Sigue en directo todas las competiciones deportivas en MSN Deportes http://deportes.es.msn.com/___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] amb2gmx for big systems
Hello, I am trying to convert a membrane-protein system from amber to gromacs using the script amb2gmx.pl (http://chemistry.csulb.edu/ffamber/tools.html). It is the dry system, only the protein and a membrane composed by DOPC, whose parameters I have got from Gaff. When I try: ./amb2gmx.pl --prmtop dry_system.top --crd dry_system.crd --outname dry_system_gmx I get an error related to the “*” symbols in the pdb (I have 253.000 atoms): (…) Argument " NATOM or " isn't numeric in multiplication (*) at ./amb2gmx.pl line 200, line 1. Argument "NRES is to" isn't numeric in multiplication (*) at ./amb2gmx.pl line 201, line 1. Argument "o big:" isn't numeric in multiplication (*) at ./amb2gmx.pl line 202, line 1. substr outside of string at ./amb2gmx.pl line 205, line 1. Use of uninitialized value in addition (+) at ./amb2gmx.pl line 205, line 1. substr outside of string at ./amb2gmx.pl line 208, line 1. Use of uninitialized value in addition (+) at ./amb2gmx.pl line 208, line 1. substr outside of string at ./amb2gmx.pl line 209, line 1. Use of uninitialized value in addition (+) at ./amb2gmx.pl line 209, line 1. substr outside of string at ./amb2gmx.pl line 212, line 1. Is there a way to transform amber systems to gromacs in spite of the “*” symbols? Has anyone transformed this type of systems? How could I save the problem? Thank you very much for your help in advance, Rebeca García Fandiño Parc Cientific de Barcelona _ Herramientas para combatir la crisis. MSN Dinero http://dinero.es.msn.com/___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Membrane: anisotropic pressure coupling
Hello, I am new in Gromacs, and I am trying to simulate the interaction between a DOPC membrane and a protein. I have equilibrated my system at constant volume and now I would like to switch to constant pressure. I think the best option for me is to use ANISOTROPIC pressure, because I want to study the ondulations produced in the membrane due to the protein. Do you recommend anisotropic pressure for this? or semiisotropic would be enough? Another question is about the values of tau_p and ref_p. I have read in the manual that in the case of anisotropic pressure I should use 6 values. Which values do you recommend to use? Should I use also 6 values for compressibility and ref_p? Pcoupl = BerendsenPcoupltype = anisotropictau_p = 2.0 2.0 2.0 2.0 2.0 2.0compressibility = 4.5e-5 4.5e-5 4.5e-5 4.5e-5 4.5e-54.5e-5ref_p = 1.0 1.0 1.0 1.0 1.0 1.0 Thank you very much for your help in advance. Best wishes, Rebeca García FandiñoParc Cientific de [EMAIL PROTECTED] _ Sigue en directo todas las competiciones deportivas en MSN Deportes http://deportes.es.msn.com/___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] topology for a membrane + protein
Hello, I am a new user of Gromacs, and I am trying to simulate a system of a membrane composed by POPC, cholesterol and sphingomyelin and a protein. I am using lipid.itp, but it includes ffgmx.itp, and I have read it is deprecated, so I am having a lot of problems to introduce the protein topology with ffG43a1 or opls, without using ffgmx.itp also for the protein. I would like to know which is the recommendation, because I am a bit confused about this, an in the case of using a different force field from the deprecated ffgmx for the protein, does anybody know where I could get the paremeters for the Berger lipids constructed with a more modern forcefield than ffgmx? I hope somebody could help me, I will really appreciate your advices. Best wishes, Rebeca Garcia Parc Cientific de Barcelona Universidad de Barcelona [EMAIL PROTECTED] Sigue de cerca las últimas tendencias y lo que más rompe MSN Vídeo Todo ruedas: información práctica y todo el glamour del mundo del motor. MSN Estilo y Tendencias _ La vida de los famosos al desnudo en MSN Entretenimiento http://entretenimiento.es.msn.com/___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
