[gmx-users] gmx dipoles and gmx potential output files detail
Hello gromacs user I am trying to calculate the various properties from the membrane simulation. As I am trying to explore the various properties which I can calculate from the trajectory using various module given in the gromacs. But I felt difficulties in understanding the various output from the gmx dipoles and gmx potential. When I search on net and in the gromacs tutorial and website, did not found detailed information regarding the output from these 2 modules. Can someone explain to me these output or provide some external source or link where these outputs are explained well in detail. Thanks in advance Mahender singh -- 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] CH3CN solvents breaking the periodic box
Hi Debashis, I haven't looked at your trajectory but I suspect this will answer your question: http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions Cara Date: Fri, 15 May 2015 12:02:31 +0530 From: debashis.sah...@gmail.com To: gmx-us...@gromacs.org Subject: Re: [gmx-users] CH3CN solvents breaking the periodic box Dear Justin, I have decreased the box size than previous box case. Now I have mentioned coupling between the system and the rest of mix solvent and ion. The trajectory of the MD is better than the earlier in this new box (water 345 and acetonitrile 48) cases. But there is a problem when I visualize the simulation in VMD, the system molecule fluctuate very suddenly from one direction to another and also tried to get out from the mix solvent box. I could not understand how to solve out the problem. If you have any idea about it please help me. I have attached the gro file and the corresponding xtc file. npt-1.xtc https://docs.google.com/file/d/0Bz4vUvGCRemJRWR3SjMtNjFhRXc/edit?usp=drive_web UN-F-3.gro https://docs.google.com/file/d/0Bz4vUvGCRemJYzFqVnUwMlF3Qms/edit?usp=drive_web with best regards, Debashis On Tue, Apr 21, 2015 at 2:35 AM, DEBASHIS SAHU debashis.sah...@gmail.com wrote: Thanks Justin for your valuable answer.. -- From: Justin Lemkul jalem...@vt.edu Sent: 4/19/2015 8:48 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] CH3CN solvents breaking the periodic box On 4/18/15 2:33 AM, Debashis Sahu wrote: Dear Gromacs users, I have faced the simulation problem in CH3CN solvent box. The box is broken in the NPT simulations and the solvent molecules also scatter. The trajectory and the pdb file is attached. I can not understand why the simulation is not running well. If any one have an idea about this problem please help me. The box seems to be much too large for the number of molecules you have. 128 solvent molecules will try to expand outward to fill the 5-nm cube you've assigned. Don't couple everything separately. http://www.gromacs.org/Documentation/Terminology/Thermostats#What_Not_To_Do -Justin npt.trr https://docs.google.com/file/d/0Bz4vUvGCRemJTWdmbnc1SGszX0E/edit?usp=drive_web UN-F-2.pdb https://docs.google.com/file/d/0Bz4vUvGCRemJZ3NhSG1iNkFxQkE/edit?usp=drive_web I have .mdp file of the energy minimization is as follow: integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 1000.0 ; Stop minimization when the maximum force 1000.0 kJ/mol/nm emstep = 0.01 ; Energy step size nsteps = 5 ; Maximum number of (minimization) steps to perform ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 1 ; Frequency to update the neighbor list and long range forces ns_type = grid ; Method to determine neighbor list (simple, grid) rlist = 1.0 ; Cut-off for making neighbor list (short range forces) coulombtype = PME ; Treatment of long range electrostatic interactions rcoulomb = 1.0 ; Short-range electrostatic cut-off rvdw = 1.0 ; Short-range Van der Waals cut-off pbc = xyz ; Periodic Boundary Conditions (yes/no) The .mdp file of NPT is as below: title = NPT Equilibration define = -DPOSRES ; position restrain ; Run parameters integrator = md; leap-frog integrator nsteps = 20 ; 2 * 5 = 100 ps dt = 0.002 ; 2 fs ; Output control nstxout = 100 ; save coordinates every 2 ps nstvout = 100 ; save velocities every 2 ps nstenergy = 100 ; save energies every 2 ps nstlog = 100 ; update log file every 2 ps nstcalcenergy= 1 ; Bond parameters continuation = no; Initial simulation 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 = 1.0 ; 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
[gmx-users] RMSD distribution calculation using g_cluster
During calculation of RMSD distribution using *g_cluster*, the Y axis of the XVG file showing the RMSD distribution denotes a.u. i.e arbitrary unit which I think probably the frequency. But it is not clear which frequency it exactly is and also kindly let me know how the calculation happened. -- *Aritra Bej* Junior Research Fellow Room No - 14 Biomolecular NMR Group Structural Biology Bioinformatics Division CSIR - Indian Institute of Chemical Biology 4, Raja S.C. Mullick Road, Jadavpur Kolkata - 700032, West Bengal, India Phone: +91-33-24995-715 Mobile: +91-9475197097 Email: aritrabej1...@gmail.com aritra...@csiriicb.in -- 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] CH3CN solvents breaking the periodic box
Dear Justin, I have decreased the box size than previous box case. Now I have mentioned coupling between the system and the rest of mix solvent and ion. The trajectory of the MD is better than the earlier in this new box (water 345 and acetonitrile 48) cases. But there is a problem when I visualize the simulation in VMD, the system molecule fluctuate very suddenly from one direction to another and also tried to get out from the mix solvent box. I could not understand how to solve out the problem. If you have any idea about it please help me. I have attached the gro file and the corresponding xtc file. npt-1.xtc https://docs.google.com/file/d/0Bz4vUvGCRemJRWR3SjMtNjFhRXc/edit?usp=drive_web UN-F-3.gro https://docs.google.com/file/d/0Bz4vUvGCRemJYzFqVnUwMlF3Qms/edit?usp=drive_web with best regards, Debashis On Tue, Apr 21, 2015 at 2:35 AM, DEBASHIS SAHU debashis.sah...@gmail.com wrote: Thanks Justin for your valuable answer.. -- From: Justin Lemkul jalem...@vt.edu Sent: 4/19/2015 8:48 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] CH3CN solvents breaking the periodic box On 4/18/15 2:33 AM, Debashis Sahu wrote: Dear Gromacs users, I have faced the simulation problem in CH3CN solvent box. The box is broken in the NPT simulations and the solvent molecules also scatter. The trajectory and the pdb file is attached. I can not understand why the simulation is not running well. If any one have an idea about this problem please help me. The box seems to be much too large for the number of molecules you have. 128 solvent molecules will try to expand outward to fill the 5-nm cube you've assigned. Don't couple everything separately. http://www.gromacs.org/Documentation/Terminology/Thermostats#What_Not_To_Do -Justin npt.trr https://docs.google.com/file/d/0Bz4vUvGCRemJTWdmbnc1SGszX0E/edit?usp=drive_web UN-F-2.pdb https://docs.google.com/file/d/0Bz4vUvGCRemJZ3NhSG1iNkFxQkE/edit?usp=drive_web I have .mdp file of the energy minimization is as follow: integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 1000.0 ; Stop minimization when the maximum force 1000.0 kJ/mol/nm emstep = 0.01 ; Energy step size nsteps = 5 ; Maximum number of (minimization) steps to perform ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 1 ; Frequency to update the neighbor list and long range forces ns_type = grid ; Method to determine neighbor list (simple, grid) rlist = 1.0 ; Cut-off for making neighbor list (short range forces) coulombtype = PME ; Treatment of long range electrostatic interactions rcoulomb = 1.0 ; Short-range electrostatic cut-off rvdw = 1.0 ; Short-range Van der Waals cut-off pbc = xyz ; Periodic Boundary Conditions (yes/no) The .mdp file of NPT is as below: title = NPT Equilibration define = -DPOSRES ; position restrain ; Run parameters integrator = md; leap-frog integrator nsteps = 20 ; 2 * 5 = 100 ps dt = 0.002 ; 2 fs ; Output control nstxout = 100 ; save coordinates every 2 ps nstvout = 100 ; save velocities every 2 ps nstenergy = 100 ; save energies every 2 ps nstlog = 100 ; update log file every 2 ps nstcalcenergy= 1 ; Bond parameters continuation = no; Initial simulation 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 = 1.0 ; 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 = V-rescale ; Weak coupling for initial equilibration tc-grps = UNK F SOL ; two coupling groups - more accurate tau_t = 0.1 0.1 0.1 ; time constant, in ps ref_t = 300 300 300 ; reference temperature, one for each group, in K ; Pressure coupling is on pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT, also weak coupling pcoupltype
[gmx-users] (no subject)
Dear All, can anyone send me the GROMACS Script file to run in cluster. Email id: sivanandam...@gmail.com M.SIVANANDAM Research Scholar Department of Physics Periyar University Salem-636 011 Mobile- 9965582730, 9042066076 -- 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] Protein+ligand complex
On 5/15/15 1:36 AM, Kashif wrote: I have done MD simulation of my protein and ligand docked complex. My protein is having 900 amino acids. When I use g_rms to analyse rmsd, the graph is too short. Currently I am simulating my protein for 5 ns. Should I increase my ns for such big protein and ligand complex? 5 ns of dynamics on a protein generally tells you nothing of any reliability. -Justin On Tue, May 12, 2015 at 4:41 AM, Kashif kashifzamir180...@gmail.com wrote: Greetings of the day, Can I use nvt.mdp and npt.mdp parameter file given in tutorial ( http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex_old/index.html) for my 5 ns production run? As the tutorial shows 100 ps nvt and npt equilibration and 1000 ps (1 ns) MD Simulation run. Which parameter should be changed if there is any problem. What are the post-simulation analysis commands used for the analysis for protein+drug complex? regards Kashif -- == 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] energy minimization problem
On 5/14/15 10:02 PM, Ming Tang wrote: Hi Justin Here is the .mdp file with position restraints, which I downloaded from the martini tutorial website. It works well with the tutorial and my small triple helix, and the grompp process does not give any warnings. Please help to have a look. Many thanks to you. define = -DPOSRES integrator = md dt = 0.02 Have you tried simply reducing the time step? 20 fs may be reasonable for a well equilibrated system, but if the run is dying early, then this is the first thing I would look at. -Justin nsteps = 5 nstxout = 0 nstvout = 0 nstlog = 1000 nstxtcout= 1000 xtc-precision= 10 cutoff-scheme=verlet coulombtype = reaction-field-zero coulomb-modifier = potential-shift-verlet rcoulomb-switch = 0.9 rcoulomb = 1.4 epsilon_r= 15 vdw-modifier = force-switch rvdw-switch = 0.9 rvdw = 1.4 tcoupl = v-rescale tc-grps = Protein W tau-t= 1.0 1.0 ref-t= 310 310 compressibility = 3e-4 ref-p= 1.0 refcoord_scaling = all pbc = xyz -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin Lemkul Sent: Friday, 15 May 2015 11:50 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] energy minimization problem On 5/14/15 9:47 PM, Ming Tang wrote: Dear Justin, I saw it in the terminal. Potential Energy = -6.3682131e+05 Maximum force = 1.8876091e+02 on atom 1147 Norm of force = 3.1155257e+00 But, how can I further minimize my protein? Minimization is not your problem. Post a full .mdp file of the run that is failing. -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. -- == 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] Sanjay (REg. Grompp error CA ATOM NOT FOUND)
On 5/15/15 6:29 AM, sanjay choubey wrote: HI, Thanks for your cooperation. Last time i asked about grompp error in running membrane dynamics simulation. THe error was atom type CA Not found. You suggested me to remove CA from DPPC.itp. But no effect still i am getting I did not suggest that. You shouldn't modify DPPC.itp in any way. the same error. Secondly may i request you to know about topol_dppc.top file. In the tutorial under the section defining protein and membrane in membrane simulation its given. What do you want to know about it? It is a very simple topology that corresponds to the hydrated 128-DPPC membrane. -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] energy minimization problem
On 5/15/15 9:32 AM, Ming Tang wrote: Reducing time helps it run longer. But 0.02ps-0.04ps is believed to be reasonable according to gromacs website. So ijust kept trying 0.02ps The time step will depend on the stability of the system, which in turn depends on how well equilibrated it is. If reducing the time step promotes stability during equilibration, that is the most obvious solution. After equilibrating for a while, try increasing the time step. -Justin Sent from my Huawei Mobile Justin Lemkul jalem...@vt.edu wrote: On 5/14/15 10:02 PM, Ming Tang wrote: Hi Justin Here is the .mdp file with position restraints, which I downloaded from the martini tutorial website. It works well with the tutorial and my small triple helix, and the grompp process does not give any warnings. Please help to have a look. Many thanks to you. define = -DPOSRES integrator = md dt = 0.02 Have you tried simply reducing the time step? 20 fs may be reasonable for a well equilibrated system, but if the run is dying early, then this is the first thing I would look at. -Justin nsteps = 5 nstxout = 0 nstvout = 0 nstlog = 1000 nstxtcout= 1000 xtc-precision= 10 cutoff-scheme=verlet coulombtype = reaction-field-zero coulomb-modifier = potential-shift-verlet rcoulomb-switch = 0.9 rcoulomb = 1.4 epsilon_r= 15 vdw-modifier = force-switch rvdw-switch = 0.9 rvdw = 1.4 tcoupl = v-rescale tc-grps = Protein W tau-t= 1.0 1.0 ref-t= 310 310 compressibility = 3e-4 ref-p= 1.0 refcoord_scaling = all pbc = xyz -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin Lemkul Sent: Friday, 15 May 2015 11:50 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] energy minimization problem On 5/14/15 9:47 PM, Ming Tang wrote: Dear Justin, I saw it in the terminal. Potential Energy = -6.3682131e+05 Maximum force = 1.8876091e+02 on atom 1147 Norm of force = 3.1155257e+00 But, how can I further minimize my protein? Minimization is not your problem. Post a full .mdp file of the run that is failing. -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. -- == 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] Why h_bond can not form
I'm so glad to tell that the question seemed to be solved after I refine the charge of Zn atom and the atoms around it. +2 may be too much for the Zn atom, and reduce the positive charge according to the results of resp calculation. Also I think the simulation could be further refined after changing to a more matchable forcefield. Thanks to Justin! You help me a lot! 在 2015-05-11 19:46:27，Justin Lemkul jalem...@vt.edu 写道： On 5/10/15 8:48 PM, 范聪 wrote: Hello everyone! I offered a picture called ask.png to illistrate my question. According to the referense papers, the H atom of the -OH group of TYR306 should form H_bond with the carbonyl O atom of the ligand. Depending on the methods used in those papers, maybe that hypothesis isn't right :) But in my simulations, the H atom turned after a very short time, towards the side chain of PHE152. I guess the reason is that, first, the positive Zn ion near the ligand's carbonyl O atom made a repulsive effect against the H atom in -OH group; second, the π-electron cloud of the side chain of PHE attracted the H atom in the -OH group of TYR306. I wouldn't put any stock in any arguments about pi electron clouds in MD simulations. QM/MM shows clearly that the assignment of +2 charge to bound metals is very crude and often a poor model of reality. As a whole, I failed to make out a real-enough simulation because the h_bond between the ligand and TYR306 did not form. This could also be a force field issue, in general. Also I have one more question: Is there any tools or solutions to calculate the hydrophobic or π-π interactions between the ligand and seleted residues of the protein, so I could make a graph of the interactions against time? You can map contacts, angles between the rings, etc. See the manual for available tools and discussions in the archive on these exact topics. -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. -- 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 problem
Reducing time helps it run longer. But 0.02ps-0.04ps is believed to be reasonable according to gromacs website. So ijust kept trying 0.02ps Sent from my Huawei Mobile Justin Lemkul jalem...@vt.edu wrote: On 5/14/15 10:02 PM, Ming Tang wrote: Hi Justin Here is the .mdp file with position restraints, which I downloaded from the martini tutorial website. It works well with the tutorial and my small triple helix, and the grompp process does not give any warnings. Please help to have a look. Many thanks to you. define = -DPOSRES integrator = md dt = 0.02 Have you tried simply reducing the time step? 20 fs may be reasonable for a well equilibrated system, but if the run is dying early, then this is the first thing I would look at. -Justin nsteps = 5 nstxout = 0 nstvout = 0 nstlog = 1000 nstxtcout= 1000 xtc-precision= 10 cutoff-scheme=verlet coulombtype = reaction-field-zero coulomb-modifier = potential-shift-verlet rcoulomb-switch = 0.9 rcoulomb = 1.4 epsilon_r= 15 vdw-modifier = force-switch rvdw-switch = 0.9 rvdw = 1.4 tcoupl = v-rescale tc-grps = Protein W tau-t= 1.0 1.0 ref-t= 310 310 compressibility = 3e-4 ref-p= 1.0 refcoord_scaling = all pbc = xyz -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin Lemkul Sent: Friday, 15 May 2015 11:50 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] energy minimization problem On 5/14/15 9:47 PM, Ming Tang wrote: Dear Justin, I saw it in the terminal. Potential Energy = -6.3682131e+05 Maximum force = 1.8876091e+02 on atom 1147 Norm of force = 3.1155257e+00 But, how can I further minimize my protein? Minimization is not your problem. Post a full .mdp file of the run that is failing. -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. -- == 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. -- 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 'Atomtype NTL not found'
On 5/15/15 4:15 PM, Ta-Chou 黃大周 wrote: Dear all, Actually, I had google for this error message, but I can't understand the answer clearly, and it seems the previous question didn't finish yet. I want to run a MD simulation with amber force field for a membrane protein. And the simulation box contains my goal membrane protein, POPC lipid and water, later will add ions. I choose the force field: amber99sb-ildn, and download the POPC.itp file from this website: http://bioinf.modares.ac.ir/software/mb/lipid_topology_files.htm In my top file, which will use in later grompp command. Top file as below: ; Include forcefield parameters #include amber99sb-ildn.ff/forcefield.itp #include POPC.itp ; Include chain topologies #include tm_Protein.itp #include tm_Protein2.itp #include tm_Protein3.itp #include tm_Protein4.itp ; Include water topology #include amber99sb-ildn.ff/spce.itp ; Include topology for ions #include amber99sb-ildn.ff/ions.itp ... After I type grompp command, it shows the error 'Atomtype NTL not found.' I found that the NTL atom-type showed in POPC.itp file. Can anybody help me to fix this problem? Or I should modify this itp file? Apparently you have to also download their Amber/Slipid force field archive to get all the parameters for those atom types. Then you'll somehow have to combine all that into one functional force field. -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] question
Hi, I am not sure anyone will be able to help, because this isn't really about Gromacs. Can you please clarify who they are and what exactly you mean by perpendicular when talking about surfactants? Also, what are those surfactants? Anyway, a reference to a representative paper and some instructions on where to quickly see what you're talking about would be nice. Once again, this isn't something Gromacs-specific. Alex On May 15, 2015 9:17 AM, Golnaz Roudsari golnaz.c...@gmail.com wrote: Dear gmx-user I want to simulate graphene and surfactants in water. In most of the paper they put surfactants perpendicular on the graphene sheet. I have problem in initial configuration. I do not know how They put them perpendicular on the graphene sheet. I can not put them random in my box because I do not have a perfect system for more than 50 ns MD run. Thank you in advance Golnaz Vahabpour -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 133, Issue 87
Golnaz, I think you're creating a bit of a mess by replying to the digest. If you don't mind, please see my answer directly to your specific question, where I will also quote your message from below. Alex GR Thank you Alex GR First of all it is better to say that I am a beginner. I follow two papers GR for my project. The authers are ''Tumala'' and ''Samalkorpi'' . GR My surfactants are mixture of CTAB and SDS. In these two papers surfactants GR were put perpendicular on the graphene sheet. because if I put surfactants GR random in the box it will take a alot of time for surfactants to transfer GR to the graphene sheet. The simulation method in the papers is GROMACS but GR authors did not mention how they loacted surfactants on the graphene sheet. GR I have written the link of the papers. I knew that it is not specifically GR Gromacs but I would like to know with which software I can make this GR change on configuration. GR http://pubs.acs.org/doi/abs/10.1021/jp077636y GR http://pubs.acs.org/doi/abs/10.1021/jp077678m GR On Fri, May 15, 2015 at 7:14 PM, GR gromacs.org_gmx-users-requ...@maillist.sys.kth.se wrote: Send gromacs.org_gmx-users mailing list submissions to gromacs.org_gmx-users@maillist.sys.kth.se To subscribe or unsubscribe via the World Wide Web, visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or, via email, send a message with subject or body 'help' to gromacs.org_gmx-users-requ...@maillist.sys.kth.se You can reach the person managing the list at gromacs.org_gmx-users-ow...@maillist.sys.kth.se When replying, please edit your Subject line so it is more specific than Re: Contents of gromacs.org_gmx-users digest... Today's Topics: 1. Re: energy minimization problem (Ming Tang) 2. Re: energy minimization problem (Justin Lemkul) 3. question (Golnaz Roudsari) 4. Re: question (Alex) 5. Re: question (abhijit Kayal) -- Message: 1 Date: Fri, 15 May 2015 13:32:04 + From: Ming Tang m21.t...@qut.edu.au To: gmx-us...@gromacs.org gmx-us...@gromacs.org Subject: Re: [gmx-users] energy minimization problem Message-ID: dv888t2enjj742h6jn4fglmx.1431696517...@email.android.com Content-Type: text/plain; charset=us-ascii Reducing time helps it run longer. But 0.02ps-0.04ps is believed to be reasonable according to gromacs website. So ijust kept trying 0.02ps Sent from my Huawei Mobile Justin Lemkul jalem...@vt.edu wrote: On 5/14/15 10:02 PM, Ming Tang wrote: Hi Justin Here is the .mdp file with position restraints, which I downloaded from the martini tutorial website. It works well with the tutorial and my small triple helix, and the grompp process does not give any warnings. Please help to have a look. Many thanks to you. define = -DPOSRES integrator = md dt = 0.02 Have you tried simply reducing the time step? 20 fs may be reasonable for a well equilibrated system, but if the run is dying early, then this is the first thing I would look at. -Justin nsteps = 5 nstxout = 0 nstvout = 0 nstlog = 1000 nstxtcout= 1000 xtc-precision= 10 cutoff-scheme=verlet coulombtype = reaction-field-zero coulomb-modifier = potential-shift-verlet rcoulomb-switch = 0.9 rcoulomb = 1.4 epsilon_r= 15 vdw-modifier = force-switch rvdw-switch = 0.9 rvdw = 1.4 tcoupl = v-rescale tc-grps = Protein W tau-t= 1.0 1.0 ref-t= 310 310 compressibility = 3e-4 ref-p= 1.0 refcoord_scaling = all pbc = xyz -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto: gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin Lemkul Sent: Friday, 15 May 2015 11:50 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] energy minimization problem On 5/14/15 9:47 PM, Ming Tang wrote: Dear Justin, I saw it in the terminal. Potential Energy = -6.3682131e+05 Maximum force = 1.8876091e+02 on atom 1147 Norm of force = 3.1155257e+00 But, how can I further minimize my protein? Minimization is not your problem. Post a full .mdp file of the run that is failing. -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
Re: [gmx-users] question
Okay, I looked at the first paper. As Abhijit said, you can manipulate any part of your input coordinates by using something like packmol. In addition, pymol and GMX itself (editconf) provides means for translation and rotation of your choosing. I think VMD has this functionality as well, although I only use it as a viewer. There's little to add at this point: learn the tool(s) of your choice and use them to manipulate your coordinates. Alex GR Thank you Alex GR First of all it is better to say that I am a beginner. I follow two papers GR for my project. The authers are ''Tumala'' and ''Samalkorpi'' . GR My surfactants are mixture of CTAB and SDS. In these two papers surfactants GR were put perpendicular on the graphene sheet. because if I put surfactants GR random in the box it will take a alot of time for surfactants to transfer GR to the graphene sheet. The simulation method in the papers is GROMACS but GR authors did not mention how they loacted surfactants on the graphene sheet. GR I have written the link of the papers. I knew that it is not specifically GR Gromacs but I would like to know with which software I can make this GR change on configuration. GR http://pubs.acs.org/doi/abs/10.1021/jp077636y GR http://pubs.acs.org/doi/abs/10.1021/jp077678m Hi, I am not sure anyone will be able to help, because this isn't really about Gromacs. Can you please clarify who "they" are and what exactly you mean by "perpendicular" when talking about surfactants? Also, what are those surfactants? Anyway, a reference to a representative paper and some instructions on where to quickly see what you're talking about would be nice. Once again, this isn't something Gromacs-specific. Alex On May 15, 2015 9:17 AM, "Golnaz Roudsari" golnaz.c...@gmail.com wrote: Dear gmx-user I want to simulate graphene and surfactants in water. In most of the paper they put surfactants perpendicular on the graphene sheet. I have problem in initial configuration. I do not know how They put them perpendicular on the graphene sheet. I can not put them random in my box because I do not have a perfect system for more than 50 ns MD run. Thank you in advance Golnaz Vahabpour -- Gromacs Users mailing list * Please search the archive athttp://www.gromacs.org/Support/Mailing_Lists/GMX-Users_Listbefore posting! * Can't post? Readhttp://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-usersor send a mail togmx-users-requ...@gromacs.org. -- Best regards, Alex mailto:nedoma...@gmail.com -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] genion error sol not continuous
Hi Justin, Thanks for your email. I have modified it and the topology looks fine to me or at least I can't see any problem with it but still genion does not like it? Would please have a look? https://drive.google.com/file/d/0B0YMTXH1gmQsSl9KbWhXaWJKc1k/view?usp=sharing https://drive.google.com/file/d/0B0YMTXH1gmQsMjlMTlNPeWJqdkk/view?usp=sharing Thanks James On Fri, May 15, 2015 at 4:36 AM, Justin Lemkul jalem...@vt.edu wrote: On 5/14/15 1:25 AM, James Lord wrote: Hi all, I am trying to neutralize this system (1HFX.gro) and genion is complaining about solvent not being continuous,then I made the 1HFX_modified.gro in which I have replaced HOH from 1HFX.gro with SOL and cut paste them at the end of the file. I am expecting gromacs to do the reordering for SOL. Am I missing anything? The topology needs to be modified in a similar manner. IIRC it is topological continuity that genion checks. -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. -- 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] Error 'Atomtype NTL not found'
Dear all, Actually, I had google for this error message, but I can't understand the answer clearly, and it seems the previous question didn't finish yet. I want to run a MD simulation with amber force field for a membrane protein. And the simulation box contains my goal membrane protein, POPC lipid and water, later will add ions. I choose the force field: amber99sb-ildn, and download the POPC.itp file from this website: http://bioinf.modares.ac.ir/software/mb/lipid_topology_files.htm In my top file, which will use in later grompp command. Top file as below: ; Include forcefield parameters #include amber99sb-ildn.ff/forcefield.itp #include POPC.itp ; Include chain topologies #include tm_Protein.itp #include tm_Protein2.itp #include tm_Protein3.itp #include tm_Protein4.itp ; Include water topology #include amber99sb-ildn.ff/spce.itp ; Include topology for ions #include amber99sb-ildn.ff/ions.itp ... After I type grompp command, it shows the error 'Atomtype NTL not found.' I found that the NTL atom-type showed in POPC.itp file. Can anybody help me to fix this problem? Or I should modify this itp file? Also, if you can't understand my question, please tell me and I will explain it clearly. Because it is important to me. Best wishes. Ta-Chou 黃大周/Ta-Chou Huang 生醫光電研究所/Institute of Biophotonics 生物醫學工程學院/School of Biomedical Science and Engineering 國立陽明大學/National Yang-Ming University 台灣台北市立農街155號2段/155, Sec. 2, Li-Nong St. Taipei, Taiwan 電話/Phone: +886-2-2826-7000#6201 手機/Mobile: +886-918-099-508 -- 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.
