[gmx-users] Re:gmx-users Digest, Vol 113, Issue 108
Dear prof. The format of parameters is convenient to the software of Amber and not to gromacs. if i use the parameters i must use some tools to convert it to the itp format for gromacs. so i use acpype to get itp format. i just doubt that i use amber99sb for protein and AM1-BBC for ligand and resp charge for cofactor. it looks like unprofessional and i don't know whether can affect the the MD . I do like this is right or not ? At 2013-09-24 18:00:04,gmx-users-requ...@gromacs.org wrote: Send gmx-users mailing list submissions to gmx-users@gromacs.org To subscribe or unsubscribe via the World Wide Web, visit http://lists.gromacs.org/mailman/listinfo/gmx-users or, via email, send a message with subject or body 'help' to gmx-users-requ...@gromacs.org You can reach the person managing the list at gmx-users-ow...@gromacs.org When replying, please edit your Subject line so it is more specific than Re: Contents of gmx-users digest... Today's Topics: 1. Re: Re: Charmm 36 forcefield with verlet cut-off scheme (Justin Lemkul) 2. Re: The charge of cofactor and ligand (Justin Lemkul) 3. Re: Fatal Error: Residue 'DMP' not found in residue topology database (Santhosh Kumar Nagarajan) 4. Re: Regarding g_sgangle index file (Venkat Reddy) -- Message: 1 Date: Mon, 23 Sep 2013 21:25:19 -0400 From: Justin Lemkul jalem...@vt.edu Subject: Re: [gmx-users] Re: Charmm 36 forcefield with verlet cut-off scheme To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 5240e9ff.1020...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 9/23/13 4:04 PM, akk5r wrote: With what was said: what do you all think of the following parameters for Charmm 36: rlist = 1.2 rlistlong = 1.4 vdwtype = cutoff rvdw-switch = 1.0 rvdw = 1.2 rcouloumb = 1.2 vdw-modifier = Potential-shift-Verlet DispCorr = No cutoff-scheme = Verlet rvdw-switch has no effect here, and I have no real hard evidence to know whether or not this will produce the same effect as the traditional settings. You would have to carefully demonstrate that what you're doing doesn't break the force field. -Justin -- == Justin A. Lemkul, Ph.D. 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 == -- Message: 2 Date: Mon, 23 Sep 2013 21:26:15 -0400 From: Justin Lemkul jalem...@vt.edu Subject: Re: [gmx-users] The charge of cofactor and ligand To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 5240ea37.4090...@vt.edu Content-Type: text/plain; charset=windows-1252; format=flowed On 9/23/13 5:10 PM, aixintiankong wrote: Dear, First i use UCSF Chimera to add hydrogens and AM1-BCC charges for the NAD+ and a ligand. when i check the charge of NAD+, I find that the distribution of charge is not correct, the N1N atom should be positive charge but the chimera give a negative. so i copy the resp charge form http://www.pharmacy.manchester.ac.uk/bryce/amber and then replace the AM1-BCC with the resp charge form http://www.pharmacy.manchester.ac.uk/bryce/amber . At last, i use acpype i ben.mol2 c user to get the nad.itp file. so the NAD+ use the RESP charge and the ligand use the AM1-BCC charges , can i do like this ? i use this method to get the NAD+.itp file? is correct or not ? Why not just use the parameters that are already published? Unless there's something wrong with them, there's no need to reinvent the wheel. -Justin -- == Justin A. Lemkul, Ph.D. 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 == -- Message: 3 Date: Mon, 23 Sep 2013 20:43:28 -0700 (PDT) From: Santhosh Kumar Nagarajan santhoshraja...@gmail.com Subject: [gmx-users] Re: Fatal Error: Residue 'DMP' not found in residue topology database To: gmx-users@gromacs.org Message-ID: 1379994208045-5011420.p...@n6.nabble.com Content-Type: text/plain; charset=us-ascii Justin.. I understand the problem.. But.. How to generate a .rtp file myself.. - Santhosh Kumar Nagarajan MTech Bioinformatics SRM University Chennai India -- View this message in context: http://gromacs.5086.x6.nabble.com/Fatal-Error-Residue-DMP-not-found-in-residue-topology-database-tp5011333p5011420.html Sent from the GROMACS Users Forum mailing list
[gmx-users] periodic surface minimization
Dear list members, I am trying to simulate an infinite layer of quartz in Gromacs. Due to my needs (afterwards I need to place a large molecule on top of it) the surface must be at least 12x12 nm^2. I generated the input files from a pdb file of the structure, and adapted the OPLS force field to my current needs, adding some compatible parameters from the literature. I am using the parameter periodic-molecules = yes in the mdp file, because if not I have a warning about inconsistent shifts. As Gromacs could not minimize the structure, I just took a smaller version of the surface compatible with the cut-off radius, with the idea to minimize it and then simply replicate it to obtain the large surface I need. Now Gromacs was able to minimize the small system, but I realized that it was not taking into account the bonded potentials across boundary conditions. I did not manage to obtain a topology file by the use of pdb2gmx which included the bonded potentials across periodic boundary conditions, so I wrote my own program to generate them. I checked that the missing interactions were properly added. I run again the simulation with the right topology file for the small system, and everything worked. The problem is that, when I replicate the minimized structure in the x and z directions to obtain the structure I need (and generating a new topology file with the right bond information, changing the simulation box size properly, etc), Gromacs still can not minimize the system, so that it does not 'explode' when I later try to minimize the system after generating a velocity for every atom, even at very low temperatures. I also tried to minimize the original, large simulation box with a proper topology file, to change the minimization method, the minimization step, tried different constraints, etc, but without success. I have been working on this problem for three weeks now and I run out of ideas, can any of you help? I copy one example of mdp I used. ;constraints = all-bonds constraints = none ; integration parameters ;integrator = l-bfgs integrator = cg ;integrator = steep dt = 0.00 nsteps = 15000 periodic-molecules = yes ; center of mass removal nstcomm = 10 comm_mode= Linear ; neighbour searching nstlist = 10 ns_type = grid pbc = xyz ;periodic boundary conditions in all directions rlist= 1.5 ; electrostatics coulombtype = PME rcoulomb = 1.5 ; van der Waals interactions vdwtype = cut-off rvdw = 1.5 DispCorr = EnerPres ;tail corrections ; Ewald parameters fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order= 4 ewald_rtol = 1e-6 optimize_fft = yes ; energy minimization emtol= 10.0 emstep = 0.01 Thanks -- View this message in context: http://gromacs.5086.x6.nabble.com/periodic-surface-minimization-tp5011423.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Use of walls combining with the PME and pressure coupling (new)
Dear all, I have sent this e-mail to the gmx-users mailing list for a few days, but without any reply until now. I'm not sure if it has something to do with the format, because the link cant be opened when I search the mailing list. So this time I use the plain text and send it once more, would anyone please help me with this? Im working on some simulations about the adsorption of protein on solid surfaces, which have slab geometry in the x-y plane. In order to reduce the amount of water molecules and at the same time to decrease the unphysical Coulomb interaction between periodic images in the z-direction, an empty layer should be added in the z-direction. To prevent the water molecules from evaporating into the vacuum layer, Im going to use the wall option. However, there are some details that Im not pretty sure about. What are your suggestions about the choice of wall_atomtype and wall_type? Is it necessary to leave some room for the two walls (or it may lead to high interaction energies between the walls and the system) and how to determine its height (in my simulations, I leave about 1.5 Angstrom, respectively)? Does it have something to do with the wall_atomtype and wall_type? When choosing nwall=2, pressure coupling and Ewald summation can be used (it is usually best to use semi-isotropic pressure coupling with x/y compressibility set to 0). It means the wall can move in the z-direction? Can the pressure coupling be used in system with fixed atoms and how can we control/calculate the pressure of the mobile phase (as it has been discussed in the paper [Biointerphases 5, 85 (2010)] using the CHARMM package)? When combining walls with the PME method, it is suggested the eward_geometry be set to 3dc and the wall_eward_zfac be 3. Does this mean there will be an empty layer whose height is 3 times the slab height added to increase the z-dimension of the box? And Im not sure about the exact meaning of the slab height; it seems to be the length/width of the slab (as described in the paper [J. Chem. Phys. 111, 3155 (1999)]). Im sorry for troubling you with so many questions. But I really need your help. Anyone could help me? Thank you!! Below is an attachment of mdp file used in my simulation work. If there is anything wrong, please be kind to point it out. Thanks again! md.mdp -- title= cyt-c on Au MD ; Run parameters integrator= md; leap-frog integrator nsteps= 1000; 2 * 1000 = 2 ps, 20 ns dt= 0.002; 2 fs comm-mode = Linear ; mode for center of mass motion removal ; Output control nstxout= 1; save coordinates every 20 ps nstvout= 1; save velocities every 20 ps nstenergy= 1; save energies every 20 ps nstlog= 1; update log file every 20 ps ; Selection of energy groups energygrps = Protein_HEM GLD ;Group(s) to write to energy file ; Bond parameters continuation= yes; Restarting after NPT constraint_algorithm = lincs; holonomic constraints, GolP has been tested with lincs only constraints= hbonds; bonds with H-atoms constrained lincs_iter= 1; accuracy of LINCS lincs_order= 4; also related to accuracy ; Neighborsearching ns_type= grid; search neighboring grid cells nstlist= 10; 20 fs rlist= 1.1; short-range neighborlist cutoff (in nm) ; Periodic boundary conditions pbc= xy; 2-D PBC ; Method for doing Van der Waals vdw-type = switch rvdw-switch = 0.9 rvdw= 1.0; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype= PME; Particle Mesh Ewald for long-range electrostatics rcoulomb= 1.1; short-range electrostatic cutoff (in nm) pme_order= 4; cubic interpolation fourierspacing= 0.12; grid spacing for FFT ewald_rtol = 1e-5 ewald_geometry = 3dc ; FFT grid size, when a value is 0 fourierspacing will be used fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 optimize_fft = yes ; Temperature coupling is on tcoupl= Nose-Hoover; Nose-Hoover thermostat tc-grps= Protein_HEM GLDWater_and_ions ; three coupling groups - more accurate tau_t= 0.50.50.5; 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 pcoupltype= semiisotropic; nonuniform scaling of box vectors tau_p= 1.01.0; time constant, in ps ref_p= 1.01.0; reference pressure, in bar compressibility = 04.5e-5; isothermal compressibility of water, bar^-1 ; Velocity generation gen_vel= no; Velocity generation is off ; Non-equilibrium MD stuff freezegrps = LOCK freezedim = Y Y Y ; WALLS ; Number of walls, type, atom types, densities and box-z scale factor for Ewald nwall = 2 wall_type = 9-3 wall_r_linpot = -1 -1 wall_atomtype = OWT3 OWT3 ; oxygen atom of TIP3P water in charmm27.ff wall_density = 33.4 33.4 wall_ewald_zfac = 3 --- Yours, sincerely! Chunwang Peng Chemistry Chemical Engineering， South China University of Technology， Tianhe District, Guangzhou, China. --
[gmx-users] walls combining with the PME and pressure coupling
Dear all, I have sent this e-mail to the gmx-users mailing list for a few days, but without any reply until now. I'm not sure if it has something to do with the format, because the link can’t be opened when I search the mailing list. So this time I use the plain text and send it once more, would anyone please help me with this? I’m working on some simulations about the adsorption of protein on solid surfaces, which have slab geometry in the x-y plane. In order to reduce the amount of water molecules and at the same time to decrease the unphysical Coulomb interaction between periodic images in the z-direction, an empty layer should be added in the z-direction. To prevent the water molecules from evaporating into the vacuum layer, I’m going to use the wall option. However, there are some details that I’m not pretty sure about. What are your suggestions about the choice of wall_atomtype and wall_type? Is it necessary to leave some room for the two walls (or it may lead to high interaction energies between the walls and the system) and how to determine its height (in my simulations, I leave about 1.5 Angstrom, respectively)? Does it have something to do with the wall_atomtype and wall_type? When choosing nwall=2, pressure coupling and Ewald summation can be used (it is usually best to use semi-isotropic pressure coupling with x/y compressibility set to 0). It means the wall can move in the z-direction? Can the pressure coupling be used in system with fixed atoms and how can we control/calculate the pressure of the mobile phase (as it has been discussed in the paper [Biointerphases 5, 85 (2010)] using the CHARMM package)? When combining walls with the PME method, it is suggested the eward_geometry be set to 3dc and the wall_eward_zfac be 3. Does this mean there will be an empty layer whose height is 3 times the slab height added to increase the z-dimension of the box? And I’m not sure about the exact meaning of the “slab height”; it seems to be the length/width of the slab (as described in the paper [J. Chem. Phys. 111, 3155 (1999)]). I’m sorry for troubling you with so many questions. But I really need your help. Anyone could help me? Thank you!! Below is an attachment of mdp file used in my simulation work. If there is anything wrong, please be kind to point it out. Thanks again! md.mdp -- title= cyt-c on Au MD ; Run parameters integrator= md; leap-frog integrator nsteps= 1000; 2 * 1000 = 2 ps, 20 ns dt= 0.002; 2 fs comm-mode = Linear ; mode for center of mass motion removal ; Output control nstxout= 1; save coordinates every 20 ps nstvout= 1; save velocities every 20 ps nstenergy= 1; save energies every 20 ps nstlog= 1; update log file every 20 ps ; Selection of energy groups energygrps= Protein_HEM GLD ;Group(s) to write to energy file ; Bond parameters continuation= yes; Restarting after NPT constraint_algorithm = lincs; holonomic constraints, GolP has been tested with lincs only constraints= hbonds; bonds with H-atoms constrained lincs_iter= 1; accuracy of LINCS lincs_order= 4; also related to accuracy ; Neighborsearching ns_type= grid; search neighboring grid cells nstlist= 10; 20 fs rlist= 1.1; short-range neighborlist cutoff (in nm) ; Periodic boundary conditions pbc= xy; 2-D PBC ; Method for doing Van der Waals vdw-type = switch rvdw-switch = 0.9 rvdw= 1.0; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype= PME; Particle Mesh Ewald for long-range electrostatics rcoulomb= 1.1; short-range electrostatic cutoff (in nm) pme_order= 4; cubic interpolation fourierspacing= 0.12; grid spacing for FFT ewald_rtol = 1e-5 ewald_geometry = 3dc ; FFT grid size, when a value is 0 fourierspacing will be used fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 optimize_fft = yes ; Temperature coupling is on tcoupl= Nose-Hoover; Nose-Hoover thermostat tc-grps= Protein_HEM GLDWater_and_ions ; three coupling groups - more accurate tau_t= 0.50.50.5; 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 pcoupltype= semiisotropic; nonuniform scaling of box vectors tau_p= 1.01.0; time constant, in ps ref_p= 1.01.0; reference pressure, in bar compressibility = 04.5e-5; isothermal compressibility of water, bar^-1 ; Velocity generation gen_vel= no; Velocity generation is off ; Non-equilibrium MD stuff freezegrps= LOCK freezedim = Y Y Y ; WALLS ; Number of walls, type, atom types, densities and box-z scale factor for Ewald nwall= 2 wall_type= 9-3 wall_r_linpot= -1 -1 wall_atomtype= OWT3 OWT3 ; oxygen atom of TIP3P water in charmm27.ff wall_density
[gmx-users] ensemble selection
Dear Justin I'm simulating gold nanoparticle interaction with protein by OPLSAA forcefield. I'm confused for selection an ensemble for my md run. I did energy minimization by NPT . then I did the MD by NVT. I did it because of studying of two paper that were similar to my project (Adsorption of histidine and histidine-containing peptides on Au(1 1 1):A molecular dynamics study by Zhen Xu, Shi-Ling Yuan and Interaction of b-Sheet Folds with a Gold Surface by Martin Hoefling, Susanna Monti, Stefano Corni). But in manual and tutorials of gromacs is proposed energy minimization should be done by NVT and NPT and then MD should be done with NPT ensemble. in your idea should I repeat my MD run by NPT ensemble? what is the difference of my result between this two? thank you Fatemeh Ramezani -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Regarding g_sgangle index file
Hello, On Tue, Sep 24, 2013 at 8:39 AM, Venkat Reddy venkat...@gmail.com wrote: I have been using the new tool gmx gangle. My actual intention is to calculate the orientation between any two same molecules (say cholesterol) throughout the trajectory and there are 40 cholesterol molecules. But I couldn't calculate it. I am getting 0 as output. My command is: gmx gangle -f traj_noPBC.xtc -s topol.tpr -n -g1 vector -g2 vector -group1 'resname CHOL and name R5 R0' -group2 'resname CHOL and name R5 R0' -oav -oall -oh In its present form, the tool cannot (easily) do what you want. It only supports calculating either a single angle, or a set of angles between fixed pairs of vectors. In your case, you are requesting the tool to calculate the R5-R0 angle between molecules 1-1, 2-2, and so on. Since for all angles, the input vectors are identical, a zero angle is the expected output. It should not be too difficult to extend the tool to do at least part of what you want, by adding an option to either calculate angles from one vector to a set of vectors (e.g., resname CHOL and resnr N and name R5 R0' and 'resname CHOL and name R5 R0'), or even to calculate the angles between all pairs of vectors. If you have programming experience and would like to extend the tool, feel free to submit your change to gerrit.gromacs.org; I'm more than happy to review and provide comments. Best regards, Teemu -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] OPLS/AA + TIP5P, anybody?
Dear GMXers, Since I am interested in interactions of lone electron pairs of water oxygen within the active site of an enzyme that I work on, I decided to give TIP5P a shot. I use OPLSAA. I run into troubles very fast trying to minimize freshly solvated system. I found on the gmx-users (http://lists.gromacs.org/pipermail/gmx-users/2008-March/032732.html) that cg and constraints don't go together when TIP5P is to be used - thats OK. It turned out, however, that I was not able to minimize my protein even with steepest descent. The system minimizes with TIP4P pretty well (emtol=1.0). In the meantime I tried to minimize short peptide - 10aa, did not work as well. What happens? The LP of water used to get too close to positively charged hydrogens (without VDW radius) on arginine. It looks like this: Step= 579, Dmax= 8.0e-03 nm, Epot= -1.40714e+05 Fmax= 1.20925e+04, atom= 171 Step= 580, Dmax= 9.6e-03 nm, Epot= -1.41193e+05 Fmax= 8.13923e+04, atom= 171 Step= 581, Dmax= 1.1e-02 nm, Epot= -1.43034e+05 Fmax= 1.03648e+06, atom= 11181 Step= 585, Dmax= 1.7e-03 nm, Epot= -1.46878e+05 Fmax= 4.23958e+06, atom= 11181 Step= 587, Dmax= 1.0e-03 nm, Epot= -1.49565e+05 Fmax= 9.43285e+06, atom= 11181 Step= 589, Dmax= 6.2e-04 nm, Epot= -1.59042e+05 Fmax= 3.55920e+07, atom= 11181 Step= 591, Dmax= 3.7e-04 nm, Epot= -1.69054e+05 Fmax= 7.79944e+07, atom= 11181 Step= 593, Dmax= 2.2e-04 nm, Epot= -1.85575e+05 Fmax= 2.27640e+08, atom= 11181 Step= 595, Dmax= 1.3e-04 nm, Epot= -2.35034e+05 Fmax= 5.88938e+08, atom= 17181 Step= 597, Dmax= 8.0e-05 nm, Epot= -2.39154e+05 Fmax= 1.22615e+09, atom= 11181 Step= 598, Dmax= 9.6e-05 nm, Epot= -2.67157e+05 Fmax= 1.96782e+09, atom= 11181 Step= 600, Dmax= 5.8e-05 nm, Epot= -4.37260e+05 Fmax= 1.08988e+10, atom= 11181 Step= 602, Dmax= 3.5e-05 nm, Epot= -4.65654e+05 Fmax= 1.29609e+10, atom= 11181 Step= 604, Dmax= 2.1e-05 nm, Epot= -1.17945e+06 Fmax= 1.31028e+11, atom= 11181 Step= 607, Dmax= 6.3e-06 nm, Epot= -3.07551e+06 Fmax= 6.04297e+11, atom= 11181 Step= 610, Dmax= 1.9e-06 nm, Epot= -4.26709e+06 Fmax= 1.61390e+12, atom= 11181 Step= 611, Dmax= 2.3e-06 nm, Epot= -4.39724e+06 Fmax= 2.14416e+12, atom= 11181 Step= 613, Dmax= 1.4e-06 nm, Epot= -1.27489e+07 Fmax= 1.03223e+13, atom= 17181 Step= 614, Dmax= 1.6e-06 nm, Epot= -5.23118e+06 Fmax= 3.18465e+12, atom= 11181 Energy minimization has stopped, but the forces havenot converged to the (...) In this example atom 171 is HH21 of ARG, and 11181 is oxygen of water that got close to this ARG. Sometimes the epot turns nan at the end. If you would like to reproduce, I put the peptide.pdb, the mdp file and the running script at http://shroom.ibb.waw.pl/tip5p . If anybody have any suggestions how to minimize (deep) with OPLSAA + TIP5P in gromacs (4.6.3 preferably...) without constraining bond lengths (which is also problematic), I will be very very grateful. Best, Grzegorz Wieczorek -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] OPLS/AA + TIP5P, anybody?
You should be able to minimize with CG and TIP5P by eliminating constraints, by making the water use a flexible molecule, e.g. define = -DFLEXIBLE (or something). Check your water .itp file for how to do it. Mark On Tue, Sep 24, 2013 at 10:25 PM, gigo g...@ibb.waw.pl wrote: Dear GMXers, Since I am interested in interactions of lone electron pairs of water oxygen within the active site of an enzyme that I work on, I decided to give TIP5P a shot. I use OPLSAA. I run into troubles very fast trying to minimize freshly solvated system. I found on the gmx-users (http://lists.gromacs.org/pipermail/gmx-users/2008-March/032732.html) that cg and constraints don't go together when TIP5P is to be used - thats OK. It turned out, however, that I was not able to minimize my protein even with steepest descent. The system minimizes with TIP4P pretty well (emtol=1.0). In the meantime I tried to minimize short peptide - 10aa, did not work as well. What happens? The LP of water used to get too close to positively charged hydrogens (without VDW radius) on arginine. It looks like this: Step= 579, Dmax= 8.0e-03 nm, Epot= -1.40714e+05 Fmax= 1.20925e+04, atom= 171 Step= 580, Dmax= 9.6e-03 nm, Epot= -1.41193e+05 Fmax= 8.13923e+04, atom= 171 Step= 581, Dmax= 1.1e-02 nm, Epot= -1.43034e+05 Fmax= 1.03648e+06, atom= 11181 Step= 585, Dmax= 1.7e-03 nm, Epot= -1.46878e+05 Fmax= 4.23958e+06, atom= 11181 Step= 587, Dmax= 1.0e-03 nm, Epot= -1.49565e+05 Fmax= 9.43285e+06, atom= 11181 Step= 589, Dmax= 6.2e-04 nm, Epot= -1.59042e+05 Fmax= 3.55920e+07, atom= 11181 Step= 591, Dmax= 3.7e-04 nm, Epot= -1.69054e+05 Fmax= 7.79944e+07, atom= 11181 Step= 593, Dmax= 2.2e-04 nm, Epot= -1.85575e+05 Fmax= 2.27640e+08, atom= 11181 Step= 595, Dmax= 1.3e-04 nm, Epot= -2.35034e+05 Fmax= 5.88938e+08, atom= 17181 Step= 597, Dmax= 8.0e-05 nm, Epot= -2.39154e+05 Fmax= 1.22615e+09, atom= 11181 Step= 598, Dmax= 9.6e-05 nm, Epot= -2.67157e+05 Fmax= 1.96782e+09, atom= 11181 Step= 600, Dmax= 5.8e-05 nm, Epot= -4.37260e+05 Fmax= 1.08988e+10, atom= 11181 Step= 602, Dmax= 3.5e-05 nm, Epot= -4.65654e+05 Fmax= 1.29609e+10, atom= 11181 Step= 604, Dmax= 2.1e-05 nm, Epot= -1.17945e+06 Fmax= 1.31028e+11, atom= 11181 Step= 607, Dmax= 6.3e-06 nm, Epot= -3.07551e+06 Fmax= 6.04297e+11, atom= 11181 Step= 610, Dmax= 1.9e-06 nm, Epot= -4.26709e+06 Fmax= 1.61390e+12, atom= 11181 Step= 611, Dmax= 2.3e-06 nm, Epot= -4.39724e+06 Fmax= 2.14416e+12, atom= 11181 Step= 613, Dmax= 1.4e-06 nm, Epot= -1.27489e+07 Fmax= 1.03223e+13, atom= 17181 Step= 614, Dmax= 1.6e-06 nm, Epot= -5.23118e+06 Fmax= 3.18465e+12, atom= 11181 Energy minimization has stopped, but the forces havenot converged to the (...) In this example atom 171 is HH21 of ARG, and 11181 is oxygen of water that got close to this ARG. Sometimes the epot turns nan at the end. If you would like to reproduce, I put the peptide.pdb, the mdp file and the running script at http://shroom.ibb.waw.pl/tip5p . If anybody have any suggestions how to minimize (deep) with OPLSAA + TIP5P in gromacs (4.6.3 preferably...) without constraining bond lengths (which is also problematic), I will be very very grateful. Best, Grzegorz Wieczorek -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] SPC with amber?
Dear all, I have been trying to evaluate a paper that used amber99 with SPC water to simulate a protein. How would this affect the results, is it important? I googled for a bit, all I found was: Amber, charmm and OPLS-AA were developed with TIP3P, and that should be the default. Except that charmm uses a TIP3P with lennard-Jones on the waters, and that should probably be the default with charmm. B.t.w., how transferable are water models between ff's? I've always been thought that they are actually non-transferable (or at least that is what I remember), making e.g. Amber/SPCe a bad option, as would gromos/tip4p.? Nobody really knows. from 2010, have things changed in 3 years, and forcefields work better with water models not developed specifically for that ff? Thanks -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] SPC with amber?
The FF+water combinations still work the same way they did 3 years ago! :-) The important question is whether validation for the observables has occurred. (And no relevant problems were seen). If the paper does not support its decision to mix and match, go and ask them why it was reasonable! Mark On Tue, Sep 24, 2013 at 10:58 PM, Rafael I. Silverman y de la Vega rsilv...@ucsc.edu wrote: Dear all, I have been trying to evaluate a paper that used amber99 with SPC water to simulate a protein. How would this affect the results, is it important? I googled for a bit, all I found was: Amber, charmm and OPLS-AA were developed with TIP3P, and that should be the default. Except that charmm uses a TIP3P with lennard-Jones on the waters, and that should probably be the default with charmm. B.t.w., how transferable are water models between ff's? I've always been thought that they are actually non-transferable (or at least that is what I remember), making e.g. Amber/SPCe a bad option, as would gromos/tip4p.? Nobody really knows. from 2010, have things changed in 3 years, and forcefields work better with water models not developed specifically for that ff? Thanks -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] SPC with amber?
Ok, thanks, I may just do that On Tue, Sep 24, 2013 at 2:42 PM, Mark Abraham mark.j.abra...@gmail.comwrote: The FF+water combinations still work the same way they did 3 years ago! :-) The important question is whether validation for the observables has occurred. (And no relevant problems were seen). If the paper does not support its decision to mix and match, go and ask them why it was reasonable! Mark On Tue, Sep 24, 2013 at 10:58 PM, Rafael I. Silverman y de la Vega rsilv...@ucsc.edu wrote: Dear all, I have been trying to evaluate a paper that used amber99 with SPC water to simulate a protein. How would this affect the results, is it important? I googled for a bit, all I found was: Amber, charmm and OPLS-AA were developed with TIP3P, and that should be the default. Except that charmm uses a TIP3P with lennard-Jones on the waters, and that should probably be the default with charmm. B.t.w., how transferable are water models between ff's? I've always been thought that they are actually non-transferable (or at least that is what I remember), making e.g. Amber/SPCe a bad option, as would gromos/tip4p.? Nobody really knows. from 2010, have things changed in 3 years, and forcefields work better with water models not developed specifically for that ff? Thanks -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: Fatal Error: Residue 'DMP' not found in residue topology database
On 9/23/13 11:43 PM, Santhosh Kumar Nagarajan wrote: Justin.. I understand the problem.. But.. How to generate a .rtp file myself.. Study existing examples, read manual section 5.6.1, and fire up a text editor. -Justin -- == Justin A. Lemkul, Ph.D. 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 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] The charge of cofactor and ligand
On 9/24/13 7:16 AM, aixintiankong wrote: Dear prof. The format of parameters is convenient to the software of Amber and not to gromacs. if i use the parameters i must use some tools to convert it to the itp format for gromacs. so i use acpype to get itp format. i just doubt that i use amber99sb for protein and AM1-BBC for ligand and resp charge for cofactor. it looks like unprofessional and i don't know whether can affect the the MD . I do like this is right or not ? The best method is to follow published protocols rather than trying make something up that you hope will be right. -Justin -- == Justin A. Lemkul, Ph.D. 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 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] ensemble selection
On 9/24/13 2:40 PM, fatemeh ramezani wrote: Dear Justin I'm simulating gold nanoparticle interaction with protein by OPLSAA forcefield. I'm confused for selection an ensemble for my md run. I did energy minimization by NPT . then I did the MD by NVT. I did it because of Let's take a step back. EM is a non-dynamical process (there are no velocities) and thus does not belong to any sort of statistical mechanical ensemble. Therefore, EM is not done under NPT, NVT, NVE etc. studying of two paper that were similar to my project (Adsorption of histidine and histidine-containing peptides on Au(1 1 1):A molecular dynamics study by Zhen Xu, Shi-Ling Yuan and Interaction of b-Sheet Folds with a Gold Surface by Martin Hoefling, Susanna Monti, Stefano Corni). But in manual and tutorials of gromacs is proposed energy minimization should be done by NVT and NPT and then MD should be done with NPT ensemble. in your idea should I repeat my MD run by NPT ensemble? what is the difference of my result between this two? You need to eliminate the perception that manuals and tutorials dictate the only way that things should be done. These are merely suggestions for accomplishing a particular task. What is true, however, is that you need to prepare and equilibrate the system such that it can be simulated under a relevant ensemble that models the experimental reality you wish to represent. A protocol that follows: EM, NVT, NPT, and production is typically robust since it introduces temperature and pressure scaling sequentially, rather than all at once, which can lead to instability. People often conduct simulations of biomolecules under NPT conditions because that's the ensemble present in a test tube in a lab or in the human body. To understand the fundamental differences between partitioning functions, ensembles, free energies, etc between different ensembles, consult any statistical mechanics or molecular modeling book. Just about all books on MM and MD feature some introductory material on these topics. -Justin -- == Justin A. Lemkul, Ph.D. 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 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] OPLS/AA + TIP5P, anybody?
Dear Mark, Thank you for your reply. Unfortunately, TIP5P is completely rigid and the FLEXIBLE define will not change it. Any other ideas? Best, g On 2013-09-24 23:51, Mark Abraham wrote: You should be able to minimize with CG and TIP5P by eliminating constraints, by making the water use a flexible molecule, e.g. define = -DFLEXIBLE (or something). Check your water .itp file for how to do it. Mark On Tue, Sep 24, 2013 at 10:25 PM, gigo g...@ibb.waw.pl wrote: Dear GMXers, Since I am interested in interactions of lone electron pairs of water oxygen within the active site of an enzyme that I work on, I decided to give TIP5P a shot. I use OPLSAA. I run into troubles very fast trying to minimize freshly solvated system. I found on the gmx-users (http://lists.gromacs.org/pipermail/gmx-users/2008-March/032732.html) that cg and constraints don't go together when TIP5P is to be used - thats OK. It turned out, however, that I was not able to minimize my protein even with steepest descent. The system minimizes with TIP4P pretty well (emtol=1.0). In the meantime I tried to minimize short peptide - 10aa, did not work as well. What happens? The LP of water used to get too close to positively charged hydrogens (without VDW radius) on arginine. It looks like this: Step= 579, Dmax= 8.0e-03 nm, Epot= -1.40714e+05 Fmax= 1.20925e+04, atom= 171 Step= 580, Dmax= 9.6e-03 nm, Epot= -1.41193e+05 Fmax= 8.13923e+04, atom= 171 Step= 581, Dmax= 1.1e-02 nm, Epot= -1.43034e+05 Fmax= 1.03648e+06, atom= 11181 Step= 585, Dmax= 1.7e-03 nm, Epot= -1.46878e+05 Fmax= 4.23958e+06, atom= 11181 Step= 587, Dmax= 1.0e-03 nm, Epot= -1.49565e+05 Fmax= 9.43285e+06, atom= 11181 Step= 589, Dmax= 6.2e-04 nm, Epot= -1.59042e+05 Fmax= 3.55920e+07, atom= 11181 Step= 591, Dmax= 3.7e-04 nm, Epot= -1.69054e+05 Fmax= 7.79944e+07, atom= 11181 Step= 593, Dmax= 2.2e-04 nm, Epot= -1.85575e+05 Fmax= 2.27640e+08, atom= 11181 Step= 595, Dmax= 1.3e-04 nm, Epot= -2.35034e+05 Fmax= 5.88938e+08, atom= 17181 Step= 597, Dmax= 8.0e-05 nm, Epot= -2.39154e+05 Fmax= 1.22615e+09, atom= 11181 Step= 598, Dmax= 9.6e-05 nm, Epot= -2.67157e+05 Fmax= 1.96782e+09, atom= 11181 Step= 600, Dmax= 5.8e-05 nm, Epot= -4.37260e+05 Fmax= 1.08988e+10, atom= 11181 Step= 602, Dmax= 3.5e-05 nm, Epot= -4.65654e+05 Fmax= 1.29609e+10, atom= 11181 Step= 604, Dmax= 2.1e-05 nm, Epot= -1.17945e+06 Fmax= 1.31028e+11, atom= 11181 Step= 607, Dmax= 6.3e-06 nm, Epot= -3.07551e+06 Fmax= 6.04297e+11, atom= 11181 Step= 610, Dmax= 1.9e-06 nm, Epot= -4.26709e+06 Fmax= 1.61390e+12, atom= 11181 Step= 611, Dmax= 2.3e-06 nm, Epot= -4.39724e+06 Fmax= 2.14416e+12, atom= 11181 Step= 613, Dmax= 1.4e-06 nm, Epot= -1.27489e+07 Fmax= 1.03223e+13, atom= 17181 Step= 614, Dmax= 1.6e-06 nm, Epot= -5.23118e+06 Fmax= 3.18465e+12, atom= 11181 Energy minimization has stopped, but the forces havenot converged to the (...) In this example atom 171 is HH21 of ARG, and 11181 is oxygen of water that got close to this ARG. Sometimes the epot turns nan at the end. If you would like to reproduce, I put the peptide.pdb, the mdp file and the running script at http://shroom.ibb.waw.pl/tip5p . If anybody have any suggestions how to minimize (deep) with OPLSAA + TIP5P in gromacs (4.6.3 preferably...) without constraining bond lengths (which is also problematic), I will be very very grateful. Best, Grzegorz Wieczorek -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
