Re: [gmx-users] rmsf question
Dear Mark, Thank you very much for your response. What I meant was to obtain a RMSF plot form PDB mediated on each residue and to compare with a RMSF plot mediated on each residue obtained from a MD trajectory. I do not compare a frame from PDB with a frame from MD trajectory. So, in the PDB file each 'frame' (MODEL) in the NMR file has the same order and number of atoms. This is also true for the MD trajectory. In the end i compare the two plots to see if the residues along the chain have comparable 'flexibility' Is necessary in this case to have a correspondence between the order of atoms in PDb and in MD trajectory? In this sense the comparison makes sense? (I mean if I do the residue mediation) (The PDB is a NMR structure and so it has the hydorgen added and no missing side chains. And, it has the same number of atoms as the gro file generated with pdb2gmx. And also the same number of atoms in the corresponding residues.) Many thanks, Andrei On Sun, Mar 14, 2010 at 3:16 PM, Mark Abraham mark.abra...@anu.edu.au wrote: On 14/03/2010 7:47 PM, Andrei Neamtu wrote: Hi, is there a rapid way to compute RMSF on an NMR ensemble from a PDB file? Yes, but that's not your problem, it seems :-) g_rmsf needs a .tpr file. Not true. Inspect the lines in g_rmsf -h describing the file types suitable for -f and -s. This is a fairly general GROMACS phenomenon. This is OK with the MD trajectories but if I want to compare MD ensemble one with the NMR RMSF ensemble fluctuations from the original PDB this is not possible. That can be a trickier proposition. You need at least the atom order to correspond to make such a comparison. If the original atom names are suitable for defining the default groups, then you might be in business. Otherwise, you'll need to construct suitable input for -s (and maybe -n), and see if it matters whether different atom names in -f matter. Mark -- gmx-users mailing list gmx-us...@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
Re: [gmx-users] rmsf question
Hi Andrei, You can do it this way. But do mind that the ensemble from NMR is not meant to reflect the Boltzmann distribution. Rather it is meant to provide a number of plausible solutions given the (positive) restraints from the experiments and the force field used for the refinement. This means that the moments of the distribution (mean and fluctuation) need not be comparable quantitatively. A more direct comparison between experiments and simulations could be obtained by comparing backbone order parameters. Cheers, Tsjerk On Mon, Mar 15, 2010 at 8:45 AM, Andrei Neamtu neamtuand...@gmail.com wrote: Dear Mark, Thank you very much for your response. What I meant was to obtain a RMSF plot form PDB mediated on each residue and to compare with a RMSF plot mediated on each residue obtained from a MD trajectory. I do not compare a frame from PDB with a frame from MD trajectory. So, in the PDB file each 'frame' (MODEL) in the NMR file has the same order and number of atoms. This is also true for the MD trajectory. In the end i compare the two plots to see if the residues along the chain have comparable 'flexibility' Is necessary in this case to have a correspondence between the order of atoms in PDb and in MD trajectory? In this sense the comparison makes sense? (I mean if I do the residue mediation) (The PDB is a NMR structure and so it has the hydorgen added and no missing side chains. And, it has the same number of atoms as the gro file generated with pdb2gmx. And also the same number of atoms in the corresponding residues.) Many thanks, Andrei On Sun, Mar 14, 2010 at 3:16 PM, Mark Abraham mark.abra...@anu.edu.au wrote: On 14/03/2010 7:47 PM, Andrei Neamtu wrote: Hi, is there a rapid way to compute RMSF on an NMR ensemble from a PDB file? Yes, but that's not your problem, it seems :-) g_rmsf needs a .tpr file. Not true. Inspect the lines in g_rmsf -h describing the file types suitable for -f and -s. This is a fairly general GROMACS phenomenon. This is OK with the MD trajectories but if I want to compare MD ensemble one with the NMR RMSF ensemble fluctuations from the original PDB this is not possible. That can be a trickier proposition. You need at least the atom order to correspond to make such a comparison. If the original atom names are suitable for defining the default groups, then you might be in business. Otherwise, you'll need to construct suitable input for -s (and maybe -n), and see if it matters whether different atom names in -f matter. Mark -- gmx-users mailing list gmx-us...@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 list gmx-us...@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 -- Tsjerk A. Wassenaar, Ph.D. Computational Chemist Medicinal Chemist Neuropharmacologist -- 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] rmsf question
On 15/03/2010 6:45 PM, Andrei Neamtu wrote: Dear Mark, Thank you very much for your response. What I meant was to obtain a RMSF plot form PDB mediated on each residue and to compare with a RMSF plot mediated on each residue obtained from a MD trajectory. I do not compare a frame from PDB with a frame from MD trajectory. Sure. I didn't imply you needed or wanted to. g_rmsf -f your.pdb -s some_suitable.file -n some.ndx g_rmsf -f your.xtc -s some_other_suitable.file -n some_other.ndx In certain cases you'll get to use the same -s or -n, or have to juggle atom orders. So, in the PDB file each 'frame' (MODEL) in the NMR file has the same order and number of atoms. This is also true for the MD trajectory. In the end i compare the two plots to see if the residues along the chain have comparable 'flexibility' Is necessary in this case to have a correspondence between the order of atoms in PDb and in MD trajectory? In this sense the comparison makes sense? (I mean if I do the residue mediation) You just need to make sure you are comparing equivalent things. If you just want (say) a C-alpha RMSF plot, then you can go ahead and do that if the index groups work. If you want all-atom RMSF then you might have some more fiddly work to do. Mark (The PDB is a NMR structure and so it has the hydorgen added and no missing side chains. And, it has the same number of atoms as the gro file generated with pdb2gmx. And also the same number of atoms in the corresponding residues.) Many thanks, Andrei On Sun, Mar 14, 2010 at 3:16 PM, Mark Abrahammark.abra...@anu.edu.au wrote: On 14/03/2010 7:47 PM, Andrei Neamtu wrote: Hi, is there a rapid way to compute RMSF on an NMR ensemble from a PDB file? Yes, but that's not your problem, it seems :-) g_rmsf needs a .tpr file. Not true. Inspect the lines in g_rmsf -h describing the file types suitable for -f and -s. This is a fairly general GROMACS phenomenon. This is OK with the MD trajectories but if I want to compare MD ensemble one with the NMR RMSF ensemble fluctuations from the original PDB this is not possible. That can be a trickier proposition. You need at least the atom order to correspond to make such a comparison. If the original atom names are suitable for defining the default groups, then you might be in business. Otherwise, you'll need to construct suitable input for -s (and maybe -n), and see if it matters whether different atom names in -f matter. Mark -- 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
Re: [gmx-users] mix berger ff with opls
On Fri, Mar 12, 2010 at 10:06:53PM -0500, chris.ne...@utoronto.ca wrote: Note that the Berger lipids were in fact developed by many people and they have come to be named by only one of the contributors. The reference that I use for my 1/8 scaling of the LJ 1-4 is: Lindahl, E., and O. Edholm. 2000. Mesoscopic undulations and thickness fluctuations in lipid bilayers from molecular dynamics simulations. Biophys. J. 79:426?433. where they state in the methods: 1,4 electrostatic inter-actions were reduced a factor of 2 and 1,4 Lennard?Jones interactions a factor of 8. I believe that this idea originated in a Jorgensen paper looking at bulk simulations of n-alkanes, but ashamedly I can't recall for sure at this moment. If you need it, I can look it up next week (let me know). And since we're quoting; From: Langmuir 2009;25:5230 Nonbonded parameters (sigma and epsilon) between OPLS/aa head group atom and Berger acyl chain 1-4 pairs are scaled by a factor 8 as recommended [opls] [opls] JACS 1988;110:1657. cheers, marc -- 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] gen_vel error
Hi everyone, Please I made an error during my simulation: I ran my simulation in the following way for many steps: grompp -v -f md.mdp -c ax.pdb -t bx.trr -e dx.edr -o ex.tpr -p fx.top mdrun -v -s ex.tpr -o gx.trr -c hx.pdb -x ix.xtc -e md.edr -g md.log But in my em.mdp, I kept: gen_vel = yes So is my simulation correct or does it generate velocities each time? I mean, what is meaningful: gen_vel or grompp -t -e ? Thank you Carla -- 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] gen_vel error
Carla Jamous wrote: Hi everyone, Please I made an error during my simulation: I ran my simulation in the following way for many steps: grompp -v -f md.mdp -c ax.pdb -t bx.trr -e dx.edr -o ex.tpr -p fx.top mdrun -v -s ex.tpr -o gx.trr -c hx.pdb -x ix.xtc -e md.edr -g md.log But in my em.mdp, I kept: gen_vel = yes So is my simulation correct or does it generate velocities each time? If you're telling grompp to re-generate velocities, then that's what it's going to do; the resulting trajectories will be discontinuous. I mean, what is meaningful: gen_vel or grompp -t -e ? If you use -t and -e in conjunction with gen_vel = yes, grompp will print a note saying that the supplied velocities are ignored and it is generating new ones. Gromacs output tries as hard as it can to help you not make errors :) The proper way to extend a simulation can be found here: http://www.gromacs.org/Documentation/How-tos/Extending_Simulations -Justin Thank you Carla -- 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/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] gen_vel error
On 16/03/2010 12:28 AM, Carla Jamous wrote: Hi everyone, Please I made an error during my simulation: I ran my simulation in the following way for many steps: grompp -v -f md.mdp -c ax.pdb -t bx.trr -e dx.edr -o ex.tpr -p fx.top mdrun -v -s ex.tpr -o gx.trr -c hx.pdb -x ix.xtc -e md.edr -g md.log But in my em.mdp, I kept: gen_vel = yes If em.mdp is for energy minimization, then this is immaterial. This kind of mismatch is why we prefer to see input lines copied from your script or terminal to your email, not filtered through your head. People's heads are fallible! So is my simulation correct or does it generate velocities each time? I mean, what is meaningful: gen_vel or grompp -t -e ? Generation over-rules those supplied to grompp. With GROMACS 4, the use of checkpoint files should be preferred. grompp and mdrun the EM, grompp and mdrun the equilibration, and then grompp for the simulation without bothering with -t or -e, since they never preserved all the state variables anyway... Then supply the equilibration checkpoint file as input to the simulation mdrun and you can have no problems with continuity. See webpage for more details on checkpointing and such. Mark -- 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] test particle insertion with PME
Hi all, has the combination of tpi (test particle insertion) and PME (particle mesh Ewald) already been implemented into any GROMACS version? Eamnuel -- 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] test particle insertion with PME
Hi, Yes, I implemented it in git master. Berk From: schn...@uni-heidelberg.de Date: Mon, 15 Mar 2010 14:52:38 +0100 To: gmx-users@gromacs.org Subject: [gmx-users] test particle insertion with PME Hi all, has the combination of tpi (test particle insertion) and PME (particle mesh Ewald) already been implemented into any GROMACS version? Eamnuel -- 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 _ New Windows 7: Simplify what you do everyday. Find the right PC for you. http://windows.microsoft.com/shop-- 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] mix berger ff with opls
Dear Bin, I think that you are getting confused here between different publications. It was the Lindahl, E., and O. Edholm. 2000. paper that you quote below, but recall that they had no protein in that work so manipulations of fudgeQQ would have been available to them. The HEDP method is pretty clear about how one gets different factors. I suggest taking a look at the non-peer reviewed .pdf file that I posted earlier as it contains more details about the method. If you still have difficulty, perhaps start from the beginning when writing your question. If you are simply concerned if the method works as advertised, then you can search the mailing list to see that I have had this type of discussion before -- the method works. Also, you can look at the plot in that .pdf file that shows some evidence that it is working alright. Chris. -- original message -- Dear Chris: Thanks a lot for your reply. That's really helpful. Now I have a further question: 1,4 electrostatic inter-actions were reduced a factor of 2 and 1,4 Lennard?Jones interactions a factor of 8. I can understand that the LJ1-4 can be reduced by simply scale epsilon in [pairtypes], how about 1,4 electrostatics? Since fudgeQQ is 1, how is the factor of 2 achieved? Thanks, Bin p.s. your paper looks really good, congrats! -- 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] g_wham error
Hi all, I'm trying to analyze a series of umbrella sampling windows, but I get the following error: Program g_wham, VERSION 4.0.7 Source code file: gmx_wham.c, line: 1397 Fatal error: Found 1 pull groups in onePREP0.tpr, but 1 data columns in onePREP0.xvg (expected 6) my .mdp file is: title= 1ns prep run, 0.0 A distance ; Run parameters integrator= md; leap-frog integrator nsteps= 50; 2 * 50 = 1ns dt= 0.002; 2 fs ; Output control nstxout= 1000; save coordinates every 2 ps nstvout= 1000; save velocities every 2 ps nstenergy= 1000; save energies every 2 ps nstlog= 1000; update log file every 2 ps ; Bond parameters continuation= yes; Restarting after NPT constraint_algorithm = lincs; holonomic constraints constraints= all-bonds; all bonds (even heavy atom-H bonds) constrained lincs_iter= 1; accuracy of LINCS lincs_order= 4; also related to accuracy ; Neighborsearching ns_type= grid; search neighboring grid cels nstlist= 5; 10 fs rlist= 1.2; short-range neighborlist cutoff (in nm) rcoulomb= 1.2; short-range electrostatic cutoff (in nm) rvdw= 1.2; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype= PME; Particle Mesh Ewald for long-range electrostatics pme_order= 4; cubic interpolation fourierspacing= 0.16; grid spacing for FFT ; Temperature coupling is on tcoupl= V-rescale; modified Berendsen thermostat tc-grps= Protein Non-Protein; two coupling groups - more accurate tau_t= 0.10.1; time constant, in ps ref_t= 300 300; reference temperature, one for each group, in K ; Pressure coupling is on pcoupl= Parrinello-Rahman; Pressure coupling on in NPT pcoupltype= isotropic; uniform scaling of box vectors tau_p= 2.0; time constant, in ps ref_p= 1.0; reference pressure, in bar compressibility = 4.5e-5; isothermal compressibility of water, bar^-1 ; Periodic boundary conditions pbc= xyz; 3-D PBC ; Dispersion correction DispCorr= EnerPres; account for cut-off vdW scheme ; Velocity generation gen_vel= yes; Velocity generation is on ; COM Pulling pull= umbrella pull_geometry= distance pull_dim= Y Y Y; or N N N pull_start= yes pull_nstxout= 1000 pull_nstfout= 1000 pull_ngroups= 1 pull_group0= COM pull_weights0= pull_pbcatom0= 0 pull_group1= MYR-C pull_weights1= pull_init1= 0.00 pull_k1= 5000 Where could this error be coming from? Thanks, Gard -- 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
