[gmx-users] Carbon monoxide topology
If you're happy that such parameters might work with your intended force field, then you only need to build them into a topology. Assuming you have some GROMACS experience, check out the relevant parts of chapters 4 and 5 of the manual. Mark On Jun 25, 2014 4:01 AM, 라지브간디 ra...@kaist.ac.kr wrote: Dear Dr. Vitaly V. Chaban, The charges and non-bonded interactions of Carbon monoxide are set to give approximate agreement with the experimental dipole quardrupole moments ( J.E. Straub, M. Karplus, Chemical Physics, 1991). According to this article, with the specific point charges and LJ parameters fit to give good agreement with the multipole moments of CO as well as lattice constant for the Myoglobin with CO structure ( Written for Charmm ff) Hence, i would like to know how do i interpret this values in charmm27 ff in gromacs? Thank you for your concern. Msg: 3 Date: Tue, 24 Jun 2014 11:26:02 +0200 From: Dr. Vitaly Chaban vvcha...@gmail.com To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Charges non-bonded interaction values usage in different force fields Message-ID: capxdd+y4fndzeel-d+wect_tmfjkq0co28dmhbsgcxgdrvc...@mail.gmail.com Content-Type: text/plain; charset=UTF-8 Can you perhaps kindly explain us how charges and non-bonded interaction values were experimentally determined? Dr. Vitaly V. Chaban On Tue, Jun 24, 2014 at 10:37 AM, Rj ra...@kaist.ac.kr wrote: Dear all, Experimentally determined charges and non-bonded interaction values for ligand atoms ( Written in charmm) can be used directly in gromacs provided charmm27.ff ? or does it need any conversion to use it in gromacs based charmm27.ff? -- 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] Query regarding Domain decomposition
Greetings I have been trying to run a few set of simulations using high number of processors. Using the tutorial - http://compchemmpi.wikispaces.com/file/view/Domaindecomposition_KKirchner_27Apr2012.pdf I have done calculations to evaluate the set of nodes which would be optimal for the protein. So the all the files are generated, but error occurs and the trajectory files remain empty with no error mentioned in the log file. Number of nodes to be used in multiple of 16 box in x and y dimension 8 nm In the error file, Reading file 400K_SIM2.tpr, VERSION 4.5.5 (single precision) Note: file tpx version 73, software tpx version 83 The number of OpenMP threads was set by environment variable OMP_NUM_THREADS to 1 Using 320 MPI processes NOTE: The load imbalance in PME FFT and solve is 116%. For optimal PME load balancing PME grid_x (54) and grid_y (54) should be divisible by #PME_nodes_x (140) and PME grid_y (54) and grid_z (54) should be divisible by #PME_nodes_y (1) mdp file for reference ; 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 cells nstlist = 5 ; 10 fs rlist = 1.0 ; short-range neighborlist cutoff (in nm) rcoulomb= 1.0 ; short-range electrostatic cutoff (in nm) rvdw= 1.0 ; 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 = nose-hoover ; nose-hoover coupling tc-grps = Protein Non-Protein ; two coupling groups - more accurate tau_t = 0.2 0.2 ; time constant, in ps ref_t = 400 400 ; reference temperature, one for each group, in K ; Pressure coupling is off pcoupl = no; ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr= EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = yes ; assign velocities from Maxwell distribution gen_temp= 400 ; temperature for Maxwell distribution gen_seed= -1; generate a random seed Kindly help. I have to run simulations at 250 to 300 processors. -- 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] Unit of force constants and adding new residue.
Dear Gromacs experts, I have a few questions regarding adding a new residue to the force field. 1) In what unit should provide force constants for stretching, bending and torsion in aminoacids.rtp file? I can't really figure that out from gromacs manual. 2) If I provide those constants and natural values of bond lengths, angles, etc. in aminoacids.rtp file, do I need to provide them in ffbonded.itp? 3) My new residue has to be connected with two natural aminoacids (Phe, Gly, etc.). Where do I specify the parameters for new atom types (of my new residue) and for these regular atom types? For example, torsion or stretching paramters where those two residues are connected. What I want to do exactly is to add parameters from Tinker format FF for a chromophore of mCherry fluorescent protein. I try to do things according to this manual: http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field I will be grateful for any help :). Best wishes, Dawid Grabarek -- 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] pdb2gmx
Thank you very much, In my analysis ,I would like to consider Hydrogen bonds involving S atom as well. I think that g_hbond is not built to manage Hydrogen bonds with S. Do you know if there are available scripts? or Could you suggest me something to solve this problem? I really appreciate your help Mirko On Friday, June 20, 2014 4:17 PM, Justin Lemkul jalem...@vt.edu wrote: On 6/20/14, 10:12 AM, mirko busato wrote: Thank you, I understood, you are right, in the .rtp file there are not neutral form for the termini. What can I do to have a neutral arginine, to have at least a total charge of 0? Because In my case I am forced to choose ARG protonated else I get the error. Fatal error In the chosen force field there is no residue type for 'ARGN' as an ending terminus Use a force field that has parameters for a neutral form. I'm sure someone has produced parameters for such a species, but they're not included in Amber99SB by default. If parameters are out there, add them (http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field), otherwise use a different force field. -Justin Thank you very much, Mirko On Thursday, June 19, 2014 3:17 PM, Justin Lemkul jalem...@vt.edu wrote: On 6/19/14, 8:59 AM, mirko busato wrote: Thank you very much for your quick reply, My peptide is only composed of amino acids, and it has a total charge of 0. My termini are NH2 and COOH (so the termini are not ionized). My force field is amber99sb. I tried to change for all atoms of my first residue (ASN) the ASN residue with the NASN residue name. In the first residue (ASN) there are the 3 atoms of N terminal . In the same way for ARG (the last residue ) with CARG. Look at the force field .rtp file - you will see that the Amber termini are predefined and they are always charged. That is an unfortunate limitation to the current implementation. I suspect someone must have produced neutral forms of the termini, but you'll have to add them yourself if you want to do such a simulation with this force field. With -inter option in the pdb2gmx command, If I select Not protonated ARG (charge 0) and the other residues with charge 0, at the end the command says: Fatal error In the chosen force field there is no residue type for 'ARGN' as an ending terminus This option chooses the side chain protonation state, not the terminus. if I select protonated ARG (charge 1) and the other residues with charge 0, I obtain charge 1 (it is obvious) but my NH2 termini is changed to NH3 and my COOH in COO. (The command works but in my case the result is wrong because the total charge has to be 0 with NH2 and COOH termini, not ionized). I don't understand if in my case I have to change ASN to NASN only for the 3 atoms in N terminal( N,H,H) and to change ARG to CARG only for the 4 atoms in C terminal ( C,O2,O1,H) or change for all atoms of the first residue (ASN), ASN with NASN, and change all atoms of the last residue (ARG) , ARG with CARG.( that I done and described before).. If this is the right way, I don't know how to obtain the right result for my peptide. As stated above, you'll have to modify the force field to add appropriate parameters or otherwise use a different force field that actually allows you to choose terminus protonation state. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu mailto:jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 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. -- 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
Re: [gmx-users] Fwd: segmentation fault on gpus
On 6/24/14, 2:11 PM, ram bio wrote: shall i do only two tc-grps protein and non-protein? Not for a membrane protein system, no. I'd say your complex, the lipids, and solvent+ions in three groups is the most common approach. -Justin On Tue, Jun 24, 2014 at 12:18 PM, Justin Lemkul jalem...@vt.edu wrote: On 6/24/14, 12:14 PM, ram bio wrote: hi Justin, Thanks, that makes sense, however I was able to use the same ligand toplogy files with earlier versions like gromacs 4.5.4 to simulate protein ligand complexes. I can simulate protein-ligand complexes with the current versions also but only for the crystal structures that have ligand bound to it, not the modelled proteins with ligands bound. So the same ligand works elsewhere, but not in a specific complex? That implicates the starting structure or the quality of the protein structure. Other notes below. and also I would appreciate any comments on the mdp file as below: title = Bilayer-500 cpp= /lib/cpp constraint_algorithm = lincs constraints= all-bonds; added lincs_iter = 1; added lincs_order= 4; added integrator = md; dt = 0.002 tinit = 0; nsteps = 100 ; 2 ns nstcomm= 500 nstxout= 5000 nstvout= 5000 nstfout= 0 nstxtcout = 500 xtc_precision = 1000 nstlog = 500 nstenergy = 500 nstlist= 50 This may work well in terms of GPU performance, but could be problematic if there are very sensitive cases. ns_type= grid; added nstcalclr = 1 ; long range interactions coulombtype= PME rlist = 1.4 rcoulomb = 1.2 rvdw = 1.2 fourierspacing = 0.16 pme_order = 4 vdw-type = Cut-off cutoff-scheme = Verlet Tcoupl = v-rescale tau_t = 0.1 0.10.1 0.1 0.1 0.1 0.1 0.1 tc-grps= Protein POPSOL NA CL LIG SOD CLA ref_t = 303 303303 303 303 303 303 303 This tc-grp setup is total nonsense. http://www.gromacs.org/Documentation/Terminology/Thermostats -Justin ; Energy monitoring energygrps = Protein POP SOL SOD CLA LIG NA CL Pcoupl = Berendsen pcoupltype = semiisotropic tau_p = 1.01.0 compressibility= 4.5e-5 4.5e-5 ref_p = 1.01.0 DispCorr= no ; added ;generate velocites is on at 293K gen_vel= yes gen_temp = 303.0 gen_seed = 478905 comm-mode = Linear comm-grps = System Thanks, Pramod On Mon, Jun 23, 2014 at 8:03 PM, Justin Lemkul jalem...@vt.edu wrote: On 6/23/14, 5:53 PM, ram bio wrote: Dear Gromacs Users, I have been trying to simulate protein-ligand complex using gromacs versions that use verlet cutoff scheme on gpus. These are some of the issues that i could resolve, and any kind of suggestion or help is appreciated. 1. With gromacs 4.6.5 i could simulate crystal structure from pdb but not modelled protein with ligand always ended up in segmentation fault. The MD run during equillibration runs for gew thousands of steps and errors out as segmentation fault, so i have to rerun using previous cpt file, for a run of 2ns to complete i have to rerun it for 7-10 times. So if the the system id not minimized, why would it go into rerun? 2. I though it could be a bug and used 4.6.3 and 5.0 release, with this trial i could equillibrate just modelled protein but not with the protein-ligand complex. The same error occurs as i mentioned above with protein-ligand complex... I am attaching my mdp file and the minimized structure that i am using for equillibration. The list doesn't accept attachments. It seems clear to me that your ligand topology is not stable. If the protein works, but the protein+ligand doesn't, what's changing? That's the likeliest source of your problem. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 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,
Re: [gmx-users] proteins break up in simulation
On 6/24/14, 11:07 PM, sunyeping wrote: Dear all,In my NPT explicit solvent simulation on the proteins with multiple chains, sometimes the protein can break up and its chains leave far from each other. We wonder if this is caused by the instability of the protein or improper simulation conditions. Could anyone give me some suggestions?Yeping Normal consequence of http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 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] topology file
On 6/25/14, 12:52 AM, Andy Chao wrote: Hi, I have a few technical questions regarding creating the topology file by using the command g_x2top. I would like to use the following GROMACS's command: g_x2top -f device.gro -ff oplsaa -o device.top to convert the .gro file to .top. The problem that I have is that the force field for carbon (graphene sheet) and C4mimNTf2 are not defined. Would you please let me know which file must be modified in order to define the force field for carbon and the elements in C4mimNTf2? ffnonbonded.itp is where you can specify nonbonded parameters for new atom types. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 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] Unit of force constants and adding new residue.
On 6/25/14, 4:42 AM, Dawid das wrote: Dear Gromacs experts, I have a few questions regarding adding a new residue to the force field. 1) In what unit should provide force constants for stretching, bending and torsion in aminoacids.rtp file? I can't really figure that out from gromacs manual. See table 5.5 in the manual; all units are listed there for all interaction types. 2) If I provide those constants and natural values of bond lengths, angles, etc. in aminoacids.rtp file, do I need to provide them in ffbonded.itp? No, values can be taken directly from the .rtp and written to the .top 3) My new residue has to be connected with two natural aminoacids (Phe, Gly, etc.). Where do I specify the parameters for new atom types (of my new residue) and for these regular atom types? For example, torsion or stretching paramters where those two residues are connected. Bonded parameters should be listed in ffbonded.itp. -Justin What I want to do exactly is to add parameters from Tinker format FF for a chromophore of mCherry fluorescent protein. I try to do things according to this manual: http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field I will be grateful for any help :). Best wishes, Dawid Grabarek -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 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] pdb2gmx
On 6/25/14, 4:44 AM, mirko busato wrote: Thank you very much, In my analysis ,I would like to consider Hydrogen bonds involving S atom as well. I think that g_hbond is not built to manage Hydrogen bonds with S. Do you know if there are available scripts? or Could you suggest me something to solve this problem? g_hbond is hard-coded to deal with certain groups, so it's not very flexible. The workaround we've used in the past is to simply rename the S atoms of interest as O in the .top file, generate a .tpr with those dummy names, and run g_hbond using that .tpr file. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 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.
[gmx-users] no domain decomposition
Hello, I have 10910 atoms ( 2160 of TiO2, 5 of sodium and formate, rest water) in my system. I am getting following error: Fatal error: There is no domain decomposition for 16 nodes that is compatible with the given box and a minimum cell size of 1.81239 nm Change the number of nodes or mdrun option -rdd Following is an excerpt of log file: Initializing Domain Decomposition on 16 nodes Dynamic load balancing: no Will sort the charge groups at every domain (re)decomposition Initial maximum inter charge-group distances: two-body bonded interactions: 1.648 nm, Bond, atoms 2161 2163 multi-body bonded interactions: 1.648 nm, Angle, atoms 2161 2163 Minimum cell size due to bonded interactions: 1.812 nm Using 0 separate PME nodes, as there are too few total nodes for efficient splitting Optimizing the DD grid for 16 cells with a minimum initial size of 1.812 nm The maximum allowed number of cells is: X 1 Y 1 Z 6 *I tried decreasing number of nodes from 48 to 16, but this error appears always. 2161 and 2163 atoms mentioned in log file excerpt above are formate atoms each of which is in a different charge group. I can't put them in same charge group, since they are different energy groups as we can see. * *Any suggestions how to interpret log file excerpt or what more can be done?* Thanks Chetan -- 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] mdrun error
On 6/25/14, 8:00 AM, Lovika Moudgil wrote: Hi Everyone...Need some help... I got the following error in my mdrun Plese help me to understand this error...What this error is all about and what should I do to remove this . --- Program mdrun, VERSION 4.6.5 Source code file: /home/itlab/Documents/gromacs/gromacs-4.6.5/src/gmxlib/smalloc.c, line: 241 Fatal error: Not enough memory. Failed to realloc 473717812 bytes for grid-index, grid-index=0x2987d008 (called from file /home/itlab/Documents/gromacs/gromacs-4.6.5/src/mdlib/nsgrid.c, line 493) For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Your hardware lacks sufficient memory to run the simulation. Either install more memory or find hardware suitable for the simulation. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 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] Query regarding Domain decomposition
On Jun 25, 2014 8:15 AM, suhani nagpal suhani.nag...@gmail.com wrote: Greetings I have been trying to run a few set of simulations using high number of processors. Using the tutorial - http://compchemmpi.wikispaces.com/file/view/Domaindecomposition_KKirchner_27Apr2012.pdf I have done calculations to evaluate the set of nodes which would be optimal for the protein. So the all the files are generated, but error occurs and the trajectory files remain empty with no error mentioned in the log file. Hard to say. The problem could be anywhere, since we don't yet know when mdrun does work... Number of nodes to be used in multiple of 16 box in x and y dimension 8 nm In the error file, Reading file 400K_SIM2.tpr, VERSION 4.5.5 (single precision) Why use a slow, old version if you want parallel performance? Note: file tpx version 73, software tpx version 83 You should prefer to use grompp whose version matches mdrun. The number of OpenMP threads was set by environment variable OMP_NUM_THREADS to 1 Using 320 MPI processes NOTE: The load imbalance in PME FFT and solve is 116%. For optimal PME load balancing PME grid_x (54) and grid_y (54) should be divisible by #PME_nodes_x (140) and PME grid_y (54) and grid_z (54) should be divisible by #PME_nodes_y (1) mdp file for reference ; 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 cells nstlist = 5 ; 10 fs rlist = 1.0 ; short-range neighborlist cutoff (in nm) rcoulomb= 1.0 ; short-range electrostatic cutoff (in nm) rvdw= 1.0 ; 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 = nose-hoover ; nose-hoover coupling tc-grps = Protein Non-Protein ; two coupling groups - more accurate tau_t = 0.2 0.2 ; time constant, in ps ref_t = 400 400 ; reference temperature, one for each group, in K ; Pressure coupling is off pcoupl = no; ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr= EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = yes ; assign velocities from Maxwell distribution gen_temp= 400 ; temperature for Maxwell distribution gen_seed= -1; generate a random seed Kindly help. I have to run simulations at 250 to 300 processors. Maybe. You can't efficiently parallelize an algorithm over arbitrary amounts of hardware. You need 100-1000 atoms per core, depending on hardware, simulation settings and GROMACS version. Mark -- 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] Free energy change upon residue mutation in protein
Hello, i'm interested in change of free energy of protein + ligand complex upon mutation. While there's some information and tutorials on decoupling of small molecules in water, i found little information on set up for free energy upon mutation, with a dated toluene - p-cresol tutorial by Gilles Pieffet and Alan E. Mark being best hit i came across. I'm having problems with my topology as well simulation parameters. My work-flow: I take a pdb reference protein with ligand and mutate it (Modeller) to represent a specific genotype. I then proceed to do EM with Gromacs on the structure (using Antechamber to parametrize the ligand, for which reason i then use amber99sb-ildn FF in the simulation). For the resulting minimized structure i want to proceed with estimation of free energy change upon L - V mutation. In the topology, for B state of the residue in question, i introduce 3 H atoms, change 6 H to dummies, do other atom substitutions/charge adaptations to valine and update all the following atom indices (topology snippet below). ; residue 76 LEU rtp LEU q 0.0 1208 N 76LEU N 1208-0.4157 14.01 ; qtot 0.5843 1209 H 76LEU H 1209 0.2719 1.008 ; qtot 0.8562 1210 CT 76LEU CA 1210-0.0518 12.01 CT -0.0875 12.01 ; qtot 0.7687 1211 H1 76LEU HA 1211 0.0922 1.008 H1 0.0969 1.008 ; qtot 0.8656 1212 CT 76LEU CB 1212-0.1102 12.01 CT 0.2985 12.01 ; qtot 1.164 1213 HC 76LEUHB1 1213 0.0457 1.008 HC -0.0297 1.008 ; qtot 1.134 1214 HC 76LEUHB2 1214 0.0457 1.008 CT -0.3192 12.01 ; qtot 0.8152 1215DUM 76LEUDUM 1215 0 1.008 HC 0.0791 1.008 ; qtot 0.8943 1216DUM 76LEUDUM 1216 0 1.008 HC 0.0791 1.008 ; qtot 0.9734 1217DUM 76LEUDUM 1217 0 1.008 HC 0.0791 1.008 ; qtot 1.052 1218 CT 76LEU CG 1218 0.3531 12.01 CT -0.3192 12.01 ; qtot 0.7333 1219 HC 76LEU HG 1219-0.0361 1.008 HC 0.0791 1.008 ; qtot 0.8124 1220 CT 76LEUCD1 1220-0.4121 12.01 HC 0.0791 1.008 ; qtot 0.8915 1221 HC 76LEU HD11 12210.1 1.008 DUM 0 1.008 ; qtot 0.8915 1222 HC 76LEU HD12 12220.1 1.008 DUM 0 1.008 ; qtot 0.8915 1223 HC 76LEU HD13 12230.1 1.008 DUM 0 1.008 ; qtot 0.8915 1224 CT 76LEUCD2 1224-0.4121 12.01 HC 0.0791 1.008 ; qtot 0.9706 1225 HC 76LEU HD21 12250.1 1.008 DUM 0 1.008 ; qtot 0.9706 1226 HC 76LEU HD22 12260.1 1.008 DUM 0 1.008 ; qtot 0.9706 1227 HC 76LEU HD23 12270.1 1.008 DUM 0 1.008 ; qtot 0.9706 1228 C 76LEU C 1228 0.5973 12.01 ; qtot 1.568 1229 O 76LEU O 1229-0.5679 16 ; qtot 1 Added bonds/angles/dihedrals snippets: [ bonds ] ; aiaj functc0c1 c2c3 1214 1215 1 1214 1216 1 1214 1217 1 [ angles ] ; aiajak functc0c1 c2c3 1212 1214 1215 1 1212 1214 1216 1 1212 1214 1217 1 1215 1214 1216 1 1215 1214 1217 1 1216 1214 1217 1 [ dihedrals ] ; aiajakal functc0c1 c2 c3c4c5 1210 1212 1214 1215 9 1210 1212 1214 1216 9 1210 1212 1214 1217 9 1213 1212 1214 1215 9 1213 1212 1214 1216 9 1213 1212 1214 1217 9 1221 1212 1214 1215 9 1221 1212 1214 1216 9 In the structure file the following dummies are added in the vicinity of HB2 (- CT) (LEU residue snipplet): 76LEU N 1208 3.836 3.954 3.263 76LEU H 1209 3.914 3.962 3.328 76LEU CA 1210 3.765 4.077 3.231 76LEU HA 1211 3.672 4.053 3.180 76LEU CB 1212 3.730 4.151 3.361 76LEUHB1 1213 3.667 4.235 3.336 76LEUHB2 1214 3.822 4.191 3.405 76LEUDUM 1215 3.910 4.191 3.379 76LEUDUM 1216 3.910 4.231 3.428 76LEUDUM 1217 3.910 4.131 3.451 76LEU CG 1218 3.661 4.064 3.468 76LEU HG 1219 3.729 3.988 3.506 76LEUCD1 1220 3.618 4.153 3.583 76LEU
Re: [gmx-users] Hamiltonian Replica Exchange
PS: [Perhaps stating the obvious] Using an overly aggressive Hamiltonian scaling will only result in bad mixing at high temperatures and therefore low efficiency, hence wasted compute time, but it should not hurt your results. It is still quite useful to ensure that you're not sampling an entirely different system at small lambda factors. -- Szilárd On Wed, Jun 25, 2014 at 6:21 PM, Szilárd Páll pall.szil...@gmail.com wrote: Hi, Next time, you should perhaps use plz, ... (and other eye-catching formatting marks); a nice mix of font colors and typefaces could also help to highlight your questions. :D On Tue, Jun 24, 2014 at 10:32 PM, Thomas Evangelidis teva...@gmail.com wrote: Greetings, I want to use the HREX implementation of GROMACS to study the dynamics of a heterodimeric protein. The structure is a two helix bundle (two helical monomers that are wrapped around each other) with disordered ends. I am mainly interested in the dynamics of the disordered ends because I know from NMR that the rest remains structured. My question is, can I scale selectively the Hamiltonian of the disordered ends whilst leaving the Hamiltonian of the rest of the protein untouched in order to preserve the dimeric structure? I'm no expert in protein simulations, so take this with a grain of salt. ;) Unless your helix bundle is rather unstable, I think your proposal is fine. However, why not try it first? Generate the scaled topologies and run the one with the highest effective temperature separately to assess the stability of the bundles. Otherwise I 'll have to impose distance and secondary structure restraints which will slow down the computations and render the dynamics of the structured part unphysical. Is it possible to increase the force constant of the harmonic restraints as lambda decreases to attenuate the stiffness of the helices? Restraints are indeed sometimes required (and the above suggested experiment should tell whether that's the case, I think), but the lucky thing in the less than ideal topology hacking-based PLUMED approach is that you will actually by definition have N different inputs which can have differences not only in the scaled interactions, but e.g. in restraint strength. The other alternative will be to use much fewer replicas (up to lambda ~0.8 to be on the safe side) thus with slower sampling. If you want to be on the safe side and you observe is a sudden change in the stability of the helix bundle from a certain lambda, you can just stick to scaling factors lower than this. Assessing what maximum lambda is reasonable is something you should probably anyway do. Cheers, Sz. thanks, Thomas -- == Thomas Evangelidis PhD student University of Athens Faculty of Pharmacy Department of Pharmaceutical Chemistry Panepistimioupoli-Zografou 157 71 Athens GREECE email: tev...@pharm.uoa.gr teva...@gmail.com website: https://sites.google.com/site/thomasevangelidishomepage/ -- 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] Calculating shifted VDW energies
Hi all,
I'm having trouble replicating the VDW energy from a shifted potential.
When I calculate unshifted potentials by hand, I get an answer that agrees
with GROMACS. When I calculate shifted potentials, I don't. I've included
the intermediate numbers I get as well as a simple GROMACS test case, and a
Python function that I was using to calculate the shifted potential. I
would really appreciate you help, as I'm probably making a simple mistake.
Thanks!
Here's what I think should be a simple example, two particles of the same
type, 1.0 nm apart
sigma = 1
epsilon = 0.25
V = 4*epsilon*sigma**6 = 1 [kJ mol^{-1}nm^6]
W = 4*epsilon*sigma**12 = 1 [kJ mol^{-1}nm^{12}]
So, V_LJ should be be W/r**12 - V/r**6 = 1/1 - 1/1 = 0. I get that when I
run a simple simulation.
Meanwhile, I think I'm doing wrong with shift functions. I'm trying to
replicate
vdwtype = Shift
rvdw_switch = 0.9
rvdw = 1.2
If I understand the manual correctly, I want to make repeated use of
equation Phi from 4.29 (and thus also need equations 4.27 and 4.30). Since
V and W are both 1 here, I want
Phi(r=1, alpha=12, r1=0.9, rc=1.2) - Phi(r=1, alpha=6, r1=0.9, rc=1.2)
If I call the first set of constants A12, B12 and C12, and the second A6,
B6, C6, I get
A12 = -( (12 + 4)*1.2 - (12+1)*0.9 ) / (1.2**(12+2) * (1.2-0.9)**2)
= -6.490547151887453
B12 = ((12 + 3)*1.2 - (12+1)*0.9) / (1.2**(12+2) * (1.2-0.9)**3) =
18.17353202528487
C12 = (1/1.2**12) - (A12/3)*(1.2-0.9)**3 - (B12/4)*(1.2-0.9)**4
= 0.13377017680040035
PHI12 = 1/1**12 - (A12/3)*(1-0.9)**3 - (B12/4)*(1-0.9)**4 - C12
= 0.8679390006162634
and
A6 = -( (6 + 4)*1.2 - (6+1)*0.9 ) / (1.2**(6+2) * (1.2-0.9)**2)
= -14.729309159553942
B6 = ((6 + 3)*1.2 - (6+1)*0.9) / (1.2**(6+2) * (1.2-0.9)**3)
= 38.761339893563004
C6 = (1/1.2**6) - (A6/3)*(1.2-0.9)**3 - (B6/4)*(1.2-0.9)**4
= 0.38897004583190453
PHI6 = 1/1**6 - (A6/3)*(1-0.9)**3 - (B6/4)*(1-0.9)**4 - C6
= 0.6149706903906076
So I think the shifted potential here should be PHI12 - PHI6
= 0.2529683102256558
Meanwhile, when I use GROMACS, I get 0.284678
I'm sure I'm making some simple mistake in my calculations, but I can't
find it. Perhaps I've misunderstood how to handle a shift function for VDW
interactions.
In order to test with GROMACS, I use the following commands:
grompp -f simple-energy.mdp -c martini-twoparticle-1.00.gro -p
martini-twoparticle-tworesi.top -o martini-twoparticle-1.00.tpr
mdrun -v -deffnm martini-twoparticle-1.00
echo 1 2 | g_energy -f martini-twoparticle-1.00.edr -s
martini-twoparticle-1.00.tpr -o martini-twoparticle-1.00.xvg
with the following files:
--- begin simple-energy.mdp ---
title= Simple Energy
integrator = md
unconstrained_start = yes
nsteps = 0
nstlist = 1
pbc = no
rlist= 100.0
coulombtype = Shift
rcoulomb_switch = 0.0
rcoulomb = 1.2
epsilon_r= 15
vdw_type = Shift
rvdw_switch = 0.9
rvdw = 1.2
--- end simple-energy.mdp ---
--- begin martini-two-particle-two-resi.top ---
#include martini-test-short.itp
[ system ]
; name
TWO PARTICLES
[ molecules ]
; name number
one 2
--- end martini-two-particle-two-resi.top ---
--- begin martini-test-short.itp ---
; Topology for test particles
[ defaults ]
; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ
1 1 no 1.0 1.0
[ atomtypes ]
;name at.num mass charge ptype V(c6) W(c12)
D 1 72.0 0.000 A 1.0 1.0
[ nonbond_params ]
; i j funda c6 c12
D D 1 1. 1.
[ moleculetype ]
; molname nrexcl
one 0
[ atoms]
;id type resnr residu atom cgnrcharge
1D1TWOD1 1 -1.00
[ bonds ]
--- end martini-test-short.itp ---
--- begin martini-twoparticle-1.00.gro ---
TWO PARTICLES
2
1ONE D1 1 0.000 0.000 0.000
2ONE D1 1 1.000 0.000 0.000
100.0 100.0 100.0
--- end martini-twoparticle-1.00.gro ---
Finally, here's the Python code I was using to try to generate shifted
potentials:
def get_switched(r,alpha,r1,rc):
unswitched = 1/r**alpha
A = -((alpha+4)*rc-(alpha+1)*r1)/(rc**(alpha+2)*(rc-r1)**2)
B = ((alpha+3)*rc-(alpha+1)*r1)/(rc**(alpha+2)*(rc-r1)**3)
C = (1/rc**alpha) - (A/3)*(rc-r1)**3 - (B/4)*(rc-r1)**4
#return (1/r) - (5/(3*rc)) + (5*r**3)/(3*rc**4) - (r**4)/(rc**5)
result = (1/r**alpha) - (A/3)*(r-r1)**3 - (B/4)*(r-r1)**4 - C
result[rrc] = 0.0
result[rr1] = unswitched[rr1]
return result
def v_vdw_switch(r,r1,rc,c12,c6):
vs12 = get_switched(r,alpha=12,r1=r1,rc=rc)
vs6 = get_switched(r,alpha=6,r1=r1,rc=rc)
v_vdw_switch = c12*vs12 - c6*vs6
return v_vdw_switch
as a side note, the above function *does* replicate the standard
electrostatics shift with r1=0.0.
Thanks,
-Michael
--
Michael
[gmx-users] hbond correspondence between hbond.log and hbmap.xpm
Hi, I'm new to gromacs and right now I'm trying to use g_hbond to analyze my trajectory. Basically, I create two selections in .ndx file and try to find hydrogen bonds between them. In the output, there is a y-axis record in hbond.xpm matrix file. The number of the elements of y-axis is the same with those in hbond.log file. I was wondering if they referred to the same thing. That is, if the first row below y-axis in hbmap.xpm telling me the hbond interaction of the first interaction in hbond.log file? Or it's the reverse? I'm asking the question because the hydrogen bond reported by g_hbond doesn't seems to be consistent with those found by pymol. Thank you! Zheng Ruan -- 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] Energy minimization has stopped, but the forces have not converged
On 6/25/14, 10:12 AM, Iris Nira Smith wrote: Hello gromacs users, I have searched the gmx-users archive and have successfully found multiple posts that provide advice on how to troubleshoot my issue. Unfortunately, after trying multiple ways to troubleshoot as suggested by each of these posts, I am still having the same issue. I successfully mutated a residue in my .pdb file using VMD mutator and am now in the minimization phase using steepest descent step-wise energy minimization. The error I keep getting is as follows: Steepest Descents: Tolerance (Fmax) = 1.0e+04 Number of steps= 2000 Step=0, Dmax= 1.0e-02 nm, Epot= 5.18534e+14 Fmax= 3.39138e+04, atom= 3228^M Step=1, Dmax= 1.0e-02 nm, Epot= 5.18534e+14 Fmax= 1.18748e+04, atom= 10021^M Step=2, Dmax= 5.0e-03 nm, Epot= 5.18534e+14 Fmax= 1.73483e+04, atom= 3228^M Step=3, Dmax= 2.5e-03 nm, Epot= 5.18534e+14 Fmax= 2.44124e+04, atom= 3228^M Step=4, Dmax= 1.2e-03 nm, Epot= 5.18534e+14 Fmax= 2.88081e+04, atom= 3228^M Step=5, Dmax= 6.2e-04 nm, Epot= 5.18534e+14 Fmax= 3.12647e+04, atom= 3228^M Step=6, Dmax= 3.1e-04 nm, Epot= 5.18534e+14 Fmax= 3.25644e+04, atom= 3228^M Step=7, Dmax= 1.6e-04 nm, Epot= 5.18534e+14 Fmax= 3.32326e+04, atom= 3228^M Step=8, Dmax= 7.8e-05 nm, Epot= 5.18534e+14 Fmax= 3.35718e+04, atom= 3228^M Step=9, Dmax= 3.9e-05 nm, Epot= 5.18534e+14 Fmax= 3.37432e+04, atom= 3228^M Step= 10, Dmax= 2.0e-05 nm, Epot= 5.18534e+14 Fmax= 3.38282e+04, atom= 3228^M Step= 11, Dmax= 9.8e-06 nm, Epot= 5.18534e+14 Fmax= 3.38707e+04, atom= 3228^M Step= 12, Dmax= 4.9e-06 nm, Epot= 5.18534e+14 Fmax= 3.38920e+04, atom= 3228^M Step= 13, Dmax= 2.4e-06 nm, Epot= 5.18534e+14 Fmax= 3.39031e+04, atom= 3228^M Step= 14, Dmax= 1.2e-06 nm, Epot= 5.18534e+14 Fmax= 3.39092e+04, atom= 3228^M Energy minimization has stopped, but the forces havenot converged to the requested precision Fmax 1 (whichmay not be possible for your system). It stoppedbecause the algorithm tried to make a new step whose sizewas too small, or there was no change in the energy sincelast step. Either way, we regard the minimization asconverged to within the available machine precision,given your starting configuration and EM parameters. Double precision normally gives you higher accuracy, butthis is often not needed for preparing to run moleculardynamics. You might need to increase your constraint accuracy, or turn off constraints altogether (set constraints = none in mdp file) writing lowest energy coordinates. Steepest Descents converged to machine precision in 15 steps, but did not reach the requested Fmax 1. Potential Energy = 5.1853375e+14 Maximum force = 3.3913793e+04 on atom 3228 Norm of force = 6.5862207e+02 I have analyzed my .gro file for steric clashes with atom 3228 (HE2 atom on a tyrosine located 20 amino acids from c-terminal tail) and the only thing that could potentially clash with it is a hydrogen atom on a nearby water which is 1.2 Angstroms away. I first moved x-coordinate of atom 3228 by 0.1nm (or 1.0 Angstrom), but the same error occurred. I then removed that entire water molecule that was near atom 3228, re-ran the energy minimization and the same error occurred. I changed the emtol from 1,000 to 10,000 even to 100,000 and the same error occurred. I then analyzed the energy using g_energy, but the following error occurred: Look at the energy terms in the .log file. Something should stick out like a sore thumb here. --- Program g_energy, VERSION 4.6.3 Source code file: /var/tmp/packages/gromacs-4.6.3/src/gmxlib/enxio.c, line: 828 Fatal error: Energy file g36r_em2.edr not recognized, maybe different CPU? For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- I finally started over and created a new configuration (.gro) file as well as a topology (.top) file, but the same error occurred. Note: I have 13 other mutant model systems that I have run minimization-equilibration successfully but this particular mutant model keeps giving me the same repeated error. The potential energy of this mutant system as well as the force on atom 3228 is rather high. Can you offer any advice or alternate suggestions to troubleshooting this error? Should I run a few steps of CG first and then SD? The fact that the energy is essentially infinite and never changes means it's an unresolvable problem. There is likely something intrinsically wrong with the coordinates or the topology. You're not missing any atoms or causing pdb2gmx to do anything strange, are you? -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences
Re: [gmx-users] cholesterol bond rotation
On 6/25/14, 11:55 AM, Michael Weiner wrote: Hello, I've built a lipid bilayer in Martini consisting of DPPC, DUPC, and cholesterol. When I try to do an energy minimization using the minimization.mdp provided in the Martini lipid bilayer tutorial (http://md.chem.rug.nl/cgmartini/index.php/bilayers), I get a large number (several dozen) of LINCS warnings. The warnings say that the bonds rotated more than 30 degrees. In each case, the two beads forming the bond are in a cholesterol molecule. When I look at the trajectory animation, I can see that these beads begin jiggling during the simulation, but there is no major change in the conformation of any cholesterol molecule. Should I be concerned, or would it be safe to ignore these warnings? During EM, these may not indicate a serious problem (bad clashes in the initial configuration can do that), but no sane dynamics simulation should produce LINCS warnings. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 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] hbond correspondence between hbond.log and hbmap.xpm
On 6/25/14, 4:04 PM, Zheng Ruan wrote: Hi, I'm new to gromacs and right now I'm trying to use g_hbond to analyze my trajectory. Basically, I create two selections in .ndx file and try to find hydrogen bonds between them. In the output, there is a y-axis record in hbond.xpm matrix file. The number of the elements of y-axis is the same with those in hbond.log file. I was wondering if they referred to the same thing. That is, if the first row below y-axis in hbmap.xpm telling me the hbond interaction of the first interaction in hbond.log file? Or it's the reverse? I'm asking the question because the hydrogen bond reported by g_hbond doesn't seems to be consistent with those found by pymol. The first line after the y-axis entry is actually the last hydrogen bond listed in hbond.ndx (and maybe the .log file; I've never used that one). The listed H-bonds are read from top-down (in order of increasing atom number) while the matrix should be interpreted as bottom-up to correspond to an increasing y-axis. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 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] no domain decomposition
Thanks, Mark. I was translating a crystal and for some reason, C atom of formate was getting displaced. Now, it's working. On Wed, Jun 25, 2014 at 7:16 AM, Mark Abraham mark.j.abra...@gmail.com wrote: Why do you have a bonded interaction whose length is 1.6nm? Mdrun is telling you that is limiting you. Mark On Jun 25, 2014 12:26 PM, Chetan Mahajan chetanv...@gmail.com wrote: Hello, I have 10910 atoms ( 2160 of TiO2, 5 of sodium and formate, rest water) in my system. I am getting following error: Fatal error: There is no domain decomposition for 16 nodes that is compatible with the given box and a minimum cell size of 1.81239 nm Change the number of nodes or mdrun option -rdd Following is an excerpt of log file: Initializing Domain Decomposition on 16 nodes Dynamic load balancing: no Will sort the charge groups at every domain (re)decomposition Initial maximum inter charge-group distances: two-body bonded interactions: 1.648 nm, Bond, atoms 2161 2163 multi-body bonded interactions: 1.648 nm, Angle, atoms 2161 2163 Minimum cell size due to bonded interactions: 1.812 nm Using 0 separate PME nodes, as there are too few total nodes for efficient splitting Optimizing the DD grid for 16 cells with a minimum initial size of 1.812 nm The maximum allowed number of cells is: X 1 Y 1 Z 6 *I tried decreasing number of nodes from 48 to 16, but this error appears always. 2161 and 2163 atoms mentioned in log file excerpt above are formate atoms each of which is in a different charge group. I can't put them in same charge group, since they are different energy groups as we can see. * *Any suggestions how to interpret log file excerpt or what more can be done?* Thanks Chetan -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] gromacs genbox SPC water population
Dear All, I have a system of a crystal slab at the center of the box surrounded by water. I am using position restraints for crystal. I am observing a weird thing that after NPT equilibration of system populated with SPC water using gromacs genbox command, some kinda hole or vacuum appears in the water layers. Let me explain with the snapshots that can be accessed from following link: https://www.dropbox.com/sh/jms49mz5w409d5p/AACUx7ek7x91Rvv0yiVW2cPEa Image 1 shows equilibrated snapshot of system with all as refcoord scaling option and water NOT from genbox command, but instead inserted manually. As we can see, there are no holes/vacuum in the box. Images 2 and 3 show the holes in the water layers. refcoord scaling option all is used and crystal is solvated by SPC water, latter generated using genbox command. Image 4 shows equilibrated snapshot of system where com option is used for refcoord scaling, and crystal is populated with SPC water from genbox command. As we see, there is a displacement of the slab from center to left, but there are no holes/vacuum in the water layers. Thus, combination of all option and genbox SPC population is problematic for some reason. Noting that slab does not move with all option, whereas it does move with com option, there is some issue with SPC water generation using genbox in gromacs. Also, I am using following settle algorithm for constraining water geometry: [ settles ] ; i funct length-oh length -hh 110.1 0.16333 Could anyone shed light? Thanks a lot! regards Chetan -- 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] gromacs genbox SPC water population
Just to be complete: I am using following command to populate system with SPC water using genbox: genbox -cp slab_wligf.gro -cs spc216.gro -vdwd 0.5 -box 3.081 3.637 11.07514 Thanks Chetan On Wed, Jun 25, 2014 at 7:48 PM, Chetan Mahajan chetanv...@gmail.com wrote: Dear All, I have a system of a crystal slab at the center of the box surrounded by water. I am using position restraints for crystal. I am observing a weird thing that after NPT equilibration of system populated with SPC water using gromacs genbox command, some kinda hole or vacuum appears in the water layers. Let me explain with the snapshots that can be accessed from following link: https://www.dropbox.com/sh/jms49mz5w409d5p/AACUx7ek7x91Rvv0yiVW2cPEa Image 1 shows equilibrated snapshot of system with all as refcoord scaling option and water NOT from genbox command, but instead inserted manually. As we can see, there are no holes/vacuum in the box. Images 2 and 3 show the holes in the water layers. refcoord scaling option all is used and crystal is solvated by SPC water, latter generated using genbox command. Image 4 shows equilibrated snapshot of system where com option is used for refcoord scaling, and crystal is populated with SPC water from genbox command. As we see, there is a displacement of the slab from center to left, but there are no holes/vacuum in the water layers. Thus, combination of all option and genbox SPC population is problematic for some reason. Noting that slab does not move with all option, whereas it does move with com option, there is some issue with SPC water generation using genbox in gromacs. Also, I am using following settle algorithm for constraining water geometry: [ settles ] ; i funct length-oh length -hh 110.1 0.16333 Could anyone shed light? Thanks a lot! regards Chetan -- 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.
