[gmx-users] gmx cluster -binary flag to get the "centroid" as the member that has max neighbours < cutoff ?
Dear users: I have a bunch of trajectories of the same system. I want to cluster them together (using gmx cluster gromos algorithm), identify the centroids, and then use gmx rms to evaluate the RMSD to the centroid of the top N clusters in each trajectory. The reason I want to do this is to be able to estimate the statistical error on the population in each cluster. The difficulty is that gmx cluster lists the "middle" structure in the cluster as the one with the smallest average RMSD to all members of the cluster. What I want is the cluster member with an RMSD <= cutoff to all cluster members. I could do it by developing the clusters with gmx cluster, then testing all members in an all-to-all RMSD evaluation with many runs through gmx rms to find the structure that is a direct neighbour (given the cutoff) of all cluster members. That seems tedious. The -binary flag to gmx cluster seems to do what I want. It's behavious is defined but there is no other documentation. Is this whas the -binary flag is for? Any better ideas? Thank you, Chris. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Internal energy
Hi gromacs user, A peptide(p), a solid surface(s) in water(w) solution are the three ingredients of my system. The total internal energy (Utot) of the system in NVT ensemble, can be defined as Utot = Upp + Uww + Upw + Usw + Ups , where the Uxy is the internal energy of interaction between x and y. Now my question is that how I can simulate each of these portion in a NVT ensemble simulation? I use the "energygrps = peptide surface water" in my mdp file, but my gmx energy -f case.edr does not contain any of those Uxy, but it has something like Coul(LJ)-SR:x-y, Coul(LJ)-14:x-y, I was wondering if the sum over these Coul(LJ):x-y would give me the Uxy? Also, is the "Total-Energy" in the gmx energy the total internal energy of the system Utot which shows up in the Helmholtz free energy, A = Utot-TS? Thanks, Kind regards, Alex -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] ligand moving out during umbrella sampling
On 5/8/17 10:00 AM, abhisek Mondal wrote: On Sun, May 7, 2017 at 11:37 PM, Justin Lemkul wrote: On 5/7/17 1:57 AM, abhisek Mondal wrote: Hi, For your ease of understanding regarding what is happening during this above said umbrella-mdrun, I have shared the trajectory video file the following link. https://drive.google.com/drive/folders/0B6O-L5Y7BiGJQ1FIc2tIRFE2dE0 Is this normal given that the mdp code being used ? I basically have no idea with this step, so please help me out. I'm using gromacs-4.6.2. Your setup is incorrect. You're applying a biasing potential only along z, so the ligand can move freely along x and y. A protein-ligand complex has spherical symmetry, so you should set the reaction coordinate to the vector connecting the ligand with some suitable subset of interacting protein residues. I don't get it. We are trying not to move our configuration (generated after pulling simulation) along the reaction coordinate, so for restraining we are supposed to set pull_rate1=0.0. Of course. But you said set pull_k = 0 which does not make sense. The pulling rate *is* zero during umbrella sampling (no net displacement, restrain to the specified distance along the reaction coordinate) and pulling force constant should be non-zero. If applying biasing potential only along z is causing movement along x and y then what if we apply the biasing potential along x,y,z ? Will it cause any good in restraining the ligand? This is how it should be done. The reaction coordinate should be suitably defined based on the geometry of the system. As I suggested before, choose some representative residues in the active site as one group and the ligand as the other. Thus defines the reaction coordinate without any presupposition of anything being aligned with a Cartesian axis, which is rarely the case. Moreover, you said previously "A protein-ligand complex has spherical symmetry, so you should set the reaction coordinate to the vector connecting the ligand with some suitable subset of interacting protein residues.". It is really unclear to me, could you please give me some examples to understand it more simply? I had pulled the ligand along -z axis, doesn't it mean that the reaction coordinate is to be that way ? The fact that I'm struggling with is to restrain the pull configurations for further sampling. The reaction coordinate is whatever you define it to be. Whether or not pulling along the z-axis makes sense depends on the orientation of the system and the intrinsic geometry. In your case, it doesn't make sense. In my case (the tutorial, the unidirectional growth of an amyloid fibril) it does make sense to use a single Cartesian axis for the SMD portion and subsequent umbrella sampling. I'm really a beginner, so maybe I'm asking stupid questions. Please give me some advise. I'm really unable to decipher the scenario in comparison to your amyloid article in JPCB. You should read the article to understand why I did what I did in the tutorial, and then move on to reading articles that are more similar to your case. These will be much more relevant to what you're doing. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Ligand Boron parameters
On 5/8/17 9:04 AM, Pedro Fernandes wrote: Good afternoon, I’m trying to do molecular dynamics (protein-ligand) with a ligand that has a boron atom. Can anyone help me or give me some information how can I do the parameterization of the ligand. The details will depend on the force field you've chosen to use for the protein. Factoring into that decision is how easy it will be to parametrize a ligand with boron, which none of the commonly used biomolecular force fields have. You'll be starting from absolute scratch with that atom type so you will want to be well versed in force field parametrization methods (beware: expert topic ahead). -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Error In Umbrella sampling.
Every time I ran through this step I needed to use -maxwarn. It raises no issues later on. On Fri, Apr 14, 2017 at 11:42 PM, Thomas Piggot wrote: > I too also fairly frequently use the -maxwarn option for this message. > Perhaps it would be better off as a grompp note rather than a warning, or > am I missing something here? This way, there isn't an encouragement for > people to use the -maxwarn option for other situations when it is less > appropriate. > > Cheers > > Tom > > > On 14/04/17 17:48, Christopher Neale wrote: > >> Yup, I use maxwarn all the time in that case. It's safe for general usage. >> >> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < >> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Anurag >> Dobhal >> Sent: 14 April 2017 12:43:18 >> To: gromacs.org_gmx-users@maillist.sys.kth.se >> Subject: [gmx-users] Error In Umbrella sampling. >> >> Dear Gromacs usrs, >> >> I am running a umbrella sampling simulation between two identical polymer >> chains in water using OPLS AA force field. My system does not have any >> charge. I have successfull generated the different configurations. >> >> While running the "gmx grompp -f npt_umbrella.mdp -c conf0.gro -p >> topol.top >> -n index.ndx -o npt0.tpr" command to genetarte the .tpr file I got the >> following warning. >> >> " You are generating velocities so I am assuming you are equilibrating a >>system. You are using Parrinello-Rahman pressure coupling, but this can >>be unstable for equilibration. If your system crashes, try >> equilibrating >>first with Berendsen pressure coupling. If you are not equilibrating >> the >>system, you can probably ignore this warning " >> >> I am following the Umbrella sampling tutorial by Bevan Lab developed by >> Justin. I have used the npt_umbrella.mdp file given in the tutorial. >> >> Is is safe to use maxwarn in this case ? or is their any solution to >> overcome this warning ? >> >> Any help will be highly appreciated. Thank you >> >> >> *Anurag Dobhal* >> *Graduate Student (Bioprocess Technology)* >> *Institute of Chemical Technology, Mumbai* >> >> -- >> >> >> *DISCLAIMER:* >> >> *This communication is intended only for the person or entity to which it >> is addressed and may contain confidential and / or privileged material. >> Any >> review, retransmission, dissemination or other use is prohibited. If you >> have received this in error, please contact the sender and delete this >> material from your computer. Any comments or statements made herein do not >> necessarily reflect those of Nanomedicine Research Group. Before opening >> the email or accessing any attachments, please check and scan for virus.* >> -- >> Gromacs Users mailing list >> >> * Please search the archive at http://www.gromacs.org/Support >> /Mailing_Lists/GMX-Users_List before posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-requ...@gromacs.org. >> > > -- > Dr Thomas Piggot > Visiting Fellow > University of Southampton, UK. > > > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/Support > /Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Abhisek Mondal *Senior Research Fellow* *Structural Biology and Bioinformatics Division* *CSIR-Indian Institute of Chemical Biology* *Kolkata 700032* *INDIA* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] ligand moving out during umbrella sampling
On Sun, May 7, 2017 at 11:37 PM, Justin Lemkul wrote: > > > On 5/7/17 1:57 AM, abhisek Mondal wrote: > >> Hi, >> >> For your ease of understanding regarding what is happening during this >> above said umbrella-mdrun, I have shared the trajectory video file the >> following link. >> https://drive.google.com/drive/folders/0B6O-L5Y7BiGJQ1FIc2tIRFE2dE0 >> >> Is this normal given that the mdp code being used ? I basically have no >> idea with this step, so please help me out. I'm using gromacs-4.6.2. >> >> > Your setup is incorrect. You're applying a biasing potential only along > z, so the ligand can move freely along x and y. A protein-ligand complex > has spherical symmetry, so you should set the reaction coordinate to the > vector connecting the ligand with some suitable subset of interacting > protein residues. I don't get it. We are trying not to move our configuration (generated after pulling simulation) along the reaction coordinate, so for restraining we are supposed to set pull_rate1=0.0. If applying biasing potential only along z is causing movement along x and y then what if we apply the biasing potential along x,y,z ? Will it cause any good in restraining the ligand? Moreover, you said previously "A protein-ligand complex has spherical symmetry, so you should set the reaction coordinate to the vector connecting the ligand with some suitable subset of interacting protein residues.". It is really unclear to me, could you please give me some examples to understand it more simply? I had pulled the ligand along -z axis, doesn't it mean that the reaction coordinate is to be that way ? The fact that I'm struggling with is to restrain the pull configurations for further sampling. I'm really a beginner, so maybe I'm asking stupid questions. Please give me some advise. I'm really unable to decipher the scenario in comparison to your amyloid article in JPCB. You're following the tutorial too literally and that's not correct. Also > do not restrain the protein (I say this weekly; not enough people are > reading the details of the tutorial and associated paper and just copying > .mdp settings...) > > -Justin > > >> On Sun, May 7, 2017 at 9:57 AM, abhisek Mondal >> wrote: >> >> Hi, >>> >>> I have completed pulling as per the tutorial stated. But having a strange >>> issue during umbrella sampling. When I execute: >>> *mpirun -np 320 /app/gromacs462/bin/mdrun_mpi -v -deffnm umbrella8 -pf >>> pullf-umbrella8.xvg -px pullx-umbrella8.xvg* >>> >>> The gro file generated at the end shows the ligand is way far compared to >>> starting position, as if another pulling is done ! >>> Please suggest me a way to tackle this issue. If this thing happens to >>> all >>> the configurations generated during pulling then how am I supposed to get >>> the PMF ? >>> >>> The md_umbrella.mdp I'm using is: >>> title = Umbrella pulling simulation >>> define = -DPOSRES >>> ; Run parameters >>> integrator = md >>> dt = 0.002 >>> tinit = 0 >>> nsteps = 500 ; 10 ns >>> nstcomm = 10 >>> ; Output parameters >>> nstxout = 5 ; every 100 ps >>> nstvout = 5 >>> 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 = Protein Non-Protein >>> tau_t = 0.5 0.5 >>> ref_t = 310 310 >>> ; Pressure coupling is on >>> Pcoupl = Parrinello-Rahman >>> pcoupltype = isotropic >>> tau_p = 1.0 >>> compressibility = 4.5e-5 >>> ref_p = 1.0 >>> refcoord_scaling = com >>> ; 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_ngroups= 1 >>> pull_group0 = Protein_chain_A >>> pull_group1 = ACO >>> pull_geometry = direction >>> pull_dim= N N Y ; pulling in Z dimension >>> pull_rate1 = 0.0 >>> pull_k1 = 1000 ; kJ mol^-1 nm^-2 >>> pull_start = yes ; define initial COM distance > 0 >>> pull_vec1 = 0 0 -1 >>> >>> My question is despite the pull_rate1 being 0.0, why the ligand is moving >>> ? Is it the pull_start or something else I'm missing here resulting in >>> such >>> a crash ? >>> >>> Your suggestions will be
[gmx-users] Ligand Boron parameters
Good afternoon, I’m trying to do molecular dynamics (protein-ligand) with a ligand that has a boron atom. Can anyone help me or give me some information how can I do the parameterization of the ligand. Best Regards, Pedro Fernandes -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] ligand moving out during umbrella sampling
On 5/7/17 2:22 PM, abhisek Mondal wrote: Hello Justin, Thank you for the explanation. I'm really new to the field so choosing factors in a bit confusion. You said in this set up the ligand can still move around X and Y direction. My question is what if I set pull_k1=0? The ligand also won't move this way. If you set pull_k1 to zero, it won't accomplish anything at all. You'll have no biasing force. You mentioned that during this run we want to restrain the ligand or don't want to change the configuration generated by pulling simulation. Is this approach right? I don't understand the second question. -Justin On May 7, 2017 11:37 PM, "Justin Lemkul" wrote: On 5/7/17 1:57 AM, abhisek Mondal wrote: Hi, For your ease of understanding regarding what is happening during this above said umbrella-mdrun, I have shared the trajectory video file the following link. https://drive.google.com/drive/folders/0B6O-L5Y7BiGJQ1FIc2tIRFE2dE0 Is this normal given that the mdp code being used ? I basically have no idea with this step, so please help me out. I'm using gromacs-4.6.2. Your setup is incorrect. You're applying a biasing potential only along z, so the ligand can move freely along x and y. A protein-ligand complex has spherical symmetry, so you should set the reaction coordinate to the vector connecting the ligand with some suitable subset of interacting protein residues. You're following the tutorial too literally and that's not correct. Also do not restrain the protein (I say this weekly; not enough people are reading the details of the tutorial and associated paper and just copying .mdp settings...) -Justin On Sun, May 7, 2017 at 9:57 AM, abhisek Mondal wrote: Hi, I have completed pulling as per the tutorial stated. But having a strange issue during umbrella sampling. When I execute: *mpirun -np 320 /app/gromacs462/bin/mdrun_mpi -v -deffnm umbrella8 -pf pullf-umbrella8.xvg -px pullx-umbrella8.xvg* The gro file generated at the end shows the ligand is way far compared to starting position, as if another pulling is done ! Please suggest me a way to tackle this issue. If this thing happens to all the configurations generated during pulling then how am I supposed to get the PMF ? The md_umbrella.mdp I'm using is: title = Umbrella pulling simulation define = -DPOSRES ; Run parameters integrator = md dt = 0.002 tinit = 0 nsteps = 500 ; 10 ns nstcomm = 10 ; Output parameters nstxout = 5 ; every 100 ps nstvout = 5 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 = Protein Non-Protein tau_t = 0.5 0.5 ref_t = 310 310 ; Pressure coupling is on Pcoupl = Parrinello-Rahman pcoupltype = isotropic tau_p = 1.0 compressibility = 4.5e-5 ref_p = 1.0 refcoord_scaling = com ; 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_ngroups= 1 pull_group0 = Protein_chain_A pull_group1 = ACO pull_geometry = direction pull_dim= N N Y ; pulling in Z dimension pull_rate1 = 0.0 pull_k1 = 1000 ; kJ mol^-1 nm^-2 pull_start = yes ; define initial COM distance > 0 pull_vec1 = 0 0 -1 My question is despite the pull_rate1 being 0.0, why the ligand is moving ? Is it the pull_start or something else I'm missing here resulting in such a crash ? Your suggestions will be highly appreciated. Thank you. -- Abhisek Mondal *Senior Research Fellow* *Structural Biology and Bioinformatics Division* *CSIR-Indian Institute of Chemical Biology* *Kolkata 700032* *INDIA* -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Maili
Re: [gmx-users] question about applying surface tension
On 5/7/17 2:56 PM, Ali Shomali wrote: Thanks so much Justin for your answer. actually I performed different simulations and compared the area per lipid with existing studies . for example I used gromacs charmm 22 for DPPC simulation and compared the results with Dr.Feller's paper. also I conducted a simulation on DMPC membrane and compared the results with existing data from doi:10.1021/jp048969n. also I performed a simulation with gromacs opls force field on octadecanol monolayer and checked the results with doi:10.1016/j.colsurfa.2012.09.025. in all of them my area per lipid value changes very little and another odd thing is that even when I apply a large surface tension , surface compresses! You're sort of indirectly applying a surface tension. You've got an x-y pressure of 600 bar, which means the membrane will be squeezed under the influence of high pressure. Note that there are actual surface tension options that you should probably be using. -Justin I've tested all the option I could think of. I would appreciate it so much if you can help me with this problem Justin thanks again Ali On Sun, May 7, 2017 at 10:34 PM, Justin Lemkul wrote: On 5/6/17 6:58 PM, Ali Shomali wrote: Hello to all dear gromacs users I've faced a problem with applying surface tension , I'm , trying to model a monolayer and I've noticed whenever I apply a surface tension although my surface tension is converged my area per lipid is wrong . i managed to model a bilayer to find out the problem and i noticed that in all my simulations my area per lipid changes are very little no matter what is surface tension nor cutoffs. but surface tension converges! i'm sending my mdp file . I will be so thankful if some one helps Sounds like a force field issue. Which parameter set are you using, and do you have evidence that it should respond correctly under such conditions? -Justin mdp file : title = DMPC NPT equilibration ; Run parameters integrator = md ; leap-frog integrator nsteps = 100 ; = 1000 ps dt = 0.001 ; 1 fs nstcomm = 10 comm-grps= SOL DMPC ; Remove COM for monolayers separately ; Output control nstxout = 1 ; save coordinates every 1.0 ps nstvout = 1 ; save velocities every 1.0 ps nstenergy = 500 ; save energies every 1.0 ps nstlog = 500 ; update log file every 1.0 ps ; Neighborsearching cutoff-scheme = Verlet ns_type = grid ; search neighboring grid cells nstlist = 10 ; 20 fs, largely irrelevant with Verlet rcoulomb = 1.4 ; short-range electrostatic cutoff (in nm) rvdw = 1.4 ; short-range van der Waals cutoff (in nm) ; Dispersion correction DispCorr = EnerPres ; account for cut-off vdW scheme ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics ; Temperature coupling is on tcoupl = berendsen ; modified Berendsen thermostat tc-grps = DMPC SOL ; two coupling groups - more accurate tau_t = 0.1 0.1 ; time constant, in ps ref_t = 330330 ; reference temperature, one for each group, in K ; Pressure coupling is on Pcoupl = berendsen tau_p = 10.0 compressibility = 4.5e-5 4.5e-5 ref_p = 600 1.0 ; Periodic boundary conditions pbc = xyz ; 3-D PBC -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support /Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] lipid / -OH oscillation period
On 5/8/17 4:32 AM, Tamas Hegedus wrote: Hi, I have a protein/lipid system. Using charmm36 ff and gromacs5.1.4. I set constraints = h-bonds because of charmm. 1. After that grompp complains about the oscillation between an O and H in the lipid. Why? It should not. Possible explanations I can imagine: - does gromacs constrain only protein h-bonds? No. - atom names are not recognized as an O-H? This is correct. grompp finds H atoms by the first character in the atom name. Since yours are "1" instead of normal elemental symbols, it does not detect 1HO2 as an H. Adjust your atom naming, otherwise these will not be constrained. 2. Moreover, it complains only 1O2 1HO2 and not 1O3 1HO3. Why? It usually collect NOTEs upto a pretty large number of notes and I do not expect to stop after this one. Identifying one problematic bond oscillation is enough to trigger the warning. So it will affect all equivalent interactions for the same reason. 3. What can I do? What should I do? My system is large (~700,000 atoms), so I do not want to decrease the time step. I would like to increase it (use the standard 0.002 ps). Changing the atom names, as indicated above, will solve this. -Justin NOTE 2 [file topol.top, line 38]: The bond in molecule-type BDM between atoms 8 1O2 and 9 1HO2 has an estimated oscillational period of 9.1e-03 ps, which is less than 10 times the time step of 1.0e-03 ps. Maybe you forgot to change the constraints mdp option. Thanks for your help and suggestion, Tamas -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] regarding posting queries in gromacs mailing list
Hi, You have already subscribed, nothing else is needed. Mark On Mon, 8 May 2017 13:44 Abhinav Srivastava (P14CHM002) < srivastav...@iitj.ac.in> wrote: > Dear Gromacs developers, > > Following is my email address for posting queries to GROMACS > srivastav...@iitj.ac.in > > Best regards, > > *Abhinav Srivastava* > *Research Scholar* > Indian Institute of Technology, Jodhpur > Rajasthan > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] regarding posting queries in gromacs mailing list
Dear Gromacs developers, Following is my email address for posting queries to GROMACS srivastav...@iitj.ac.in Best regards, *Abhinav Srivastava* *Research Scholar* Indian Institute of Technology, Jodhpur Rajasthan -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] lipid / -OH oscillation period
Hi, I have a protein/lipid system. Using charmm36 ff and gromacs5.1.4. I set constraints = h-bonds because of charmm. 1. After that grompp complains about the oscillation between an O and H in the lipid. Why? It should not. Possible explanations I can imagine: - does gromacs constrain only protein h-bonds? - atom names are not recognized as an O-H? 2. Moreover, it complains only 1O2 1HO2 and not 1O3 1HO3. Why? It usually collect NOTEs upto a pretty large number of notes and I do not expect to stop after this one. 3. What can I do? What should I do? My system is large (~700,000 atoms), so I do not want to decrease the time step. I would like to increase it (use the standard 0.002 ps). NOTE 2 [file topol.top, line 38]: The bond in molecule-type BDM between atoms 8 1O2 and 9 1HO2 has an estimated oscillational period of 9.1e-03 ps, which is less than 10 times the time step of 1.0e-03 ps. Maybe you forgot to change the constraints mdp option. Thanks for your help and suggestion, Tamas -- Tamas Hegedus, PhD Senior Research Fellow MTA-SE Molecular Biophysics Research Group Hungarian Academy of Sciences | phone: (36) 1-459 1500/60233 Semmelweis University | fax: (36) 1-266 6656 Tuzolto utca 37-47 | mailto:ta...@hegelab.org Budapest, 1094, Hungary| http://www.hegelab.org -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
