Re: [gmx-users] Distance restrain with dummy atom
Dear Justin, Thanks for the reply. As you suggested I have tried with flat-bottomed position restraint. Unfortunately, the water molecules were seen to be moving to vacuum that leads to membrane distortion. The methodology I adopted is as follows, 1. I done 5 ns equilibration of protein-membrane-water system. Later, I added ions to upper water layer. The box dimension of equilibrated system is 112.347 112.347 126.531 90.00 90.00 90.00. 2. Then I added a ~12nm vacuum slab along z-axis above and below the membrane using editconf command - editconf -f input.gro -o ouput.gro -c -box 11.2347 11.2347 37.9593 3. The 'output.gro' file from above step used for flat-bottomed position restraint simulation, where flat-bottomed position restraint applied on water and ions . The topology file looks as shown below, ** #include POT.itp #ifdef POSRES_ION ; Position restraint for potassium [ position_restraints ] ; i funct g r k 12 5 1 1000 #endif #include CL.itp #ifdef POSRES_ION ; Position restraint for chloride [ position_restraints ] ; i funct g r k 12 5 1 1000 #endif ; Include water topology #include charmm36-jun2015.ff/tip3p.itp #ifdef POSRES_WATER ; Position restraint for water [ position_restraints ] ; i funct g r k 12 5 1 1000 22 5 1 1000 32 5 1 1000 #endif * Here, I used layer geometry along z-axis and thickness of 1 nm. I have even tried with using thickness of half of the box length ( where the box length is excluded of vacuum slab) and also with restraining water oxygen alone. Unfortunately, all my trials has lead to water molecules flying to vacuum and membrane get distorted. Below is the mdp file is used for the simulation, ** define = -DPOSRES_ION -DPOSRES_WATER integrator = md dt = 0.001 nsteps = 1 nstlog = 1000 nstxout = 1000 nstvout = 1000 nstfout = 1000 nstcalcenergy = 100 nstenergy = 1000 ; cutoff-scheme = Verlet nstlist = 20 rlist = 1.2 coulombtype = pme rcoulomb= 1.2 vdwtype = Cut-off vdw-modifier= Force-switch rvdw_switch = 1.0 rvdw= 1.2 ; ewald-geometry = 3dc pbc = xyz ; tcoupl = V-rescale tc_grps = Protein POPC Cal_CL_SOL tau_t = 0.50.5 0.5 ref_t = 305.0305.0305.0 ; constraints = h-bonds constraint_algorithm= LINCS ; nstcomm = 100 comm_mode = linear comm_grps = Protein_POPC Cal_CL_SOL ; gen-vel = yes gen-temp= 305.0 gen-seed= -1 ; refcoord_scaling= com ** Can you please help me to figure out what is going wrong with the position restraint and simulation? Many thanks in advance Anu On Wed, Aug 12, 2015 at 12:44 AM, Justin Lemkul jalem...@vt.edu wrote: On 8/11/15 11:06 AM, anu chandra wrote: Dear Justin, Thanks for your quick reply. I am trying to run membrane protein simulation with slab geometry and EW3DC method (ewald-geometry = 3dc), due to ion asymmetry in the system. Following the article http://www.cell.com/biophysj/abstract/S0006-3495%2803%2974458-0?mobileUi=0 , I have set up my system with extended Z-dimension and used pbc = xyz. Unfortunately, when I carry out equilibration with EW3DC method and pbc=xyz, the membrane got distorted and become leaky. So, I trying to restraining water within a specific distance might help me to come out this problem. Below, I just copied the mdp file I am using for equilibration with slab geometry. If possible, please have a look and let me know valuable suggestion in this regard. Use walls or a flat-bottom restraint and normal PBC/PME. -Justin define = -DPOSRES_ON integrator = md dt = 0.001 nsteps = 25000 nstlog = 1000 nstxout = 1000 nstvout = 1000 nstfout = 1000 nstcalcenergy = 100 nstenergy = 1000 ; cutoff-scheme = Verlet nstlist = 20 rlist = 1.2 coulombtype = pme rcoulomb= 1.2 vdwtype = Cut-off vdw-modifier= Force-switch rvdw_switch = 1.0
Re: [gmx-users] Pdb file
I mean potential energy of system (1600 argon atoms) is positive after energy mininization . On 12 Aug 2015 16:58, Vitaly V. Chaban vvcha...@gmail.com wrote: L_BFGS On Tue, Aug 11, 2015 at 11:37 PM, Sunil Ghimire ghimiresuni...@gmail.com wrote: I created the pdb file by genconf but the system was not minimized, i got positive potential energy. What may be the problem? On 11 Aug 2015 19:38, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, gmx genconf on a small box with a single argon is a useful starting point. Mark On Tue, Aug 11, 2015 at 3:16 PM Sunil Ghimire ghimiresuni...@gmail.com wrote: How can i create the .pdb file for 1600 atoms of argon ? -- 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. -- 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] Charged group problem
Thank you Justin, as friendly as ever! Adriana *** Dra. Adriana D. Garro Química Medicinal Facultad de Química, Bioquímica y Farmacia Universidad Nacional de San Luis IMASL-CONICET San Luis, Argentina Tel..:+54 266 4424689 int 6153 e-mail...: adga...@unsl.edu.ar e-mail...: adrianagarr...@gmail.com ** 2015-08-12 17:27 GMT-03:00 Justin Lemkul jalem...@vt.edu: On 8/12/15 9:30 AM, Adriana Garro wrote: Dear users, My system contains peptide + TFE + water in an octahedron box. I am using oplsaa.ff I am trying to do EM but running this command grompp -f em.mdp -c C22_TFE-W.gro -p topol.top -o em.tpr the next error message come up WARNING 1 [file em.mdp]: The sum of the two largest charge group radii (2.045171) is larger than rlist (1.00) I am afraid of changing the em.mdp parameters because as I understand these are the correct for my force field. I'd really appreciate suggestions! Assign smaller charge groups (fewer atoms), or use the Verlet cutoff scheme, for which charge groups are irrelevant (it's more accurate than the old group scheme, anyway). -Justin Thanks in advance Adriana here a part of the em.mdp file nstlist= 1 ns_type= grid rlist = 1.0 coulombtype= PME; Use particle-mesh ewald rcoulomb = 1.0 rvdw = 1.0 I read that large charge groups indicate that a fair number of atoms have been included in the same charge group. Usually only two or three atoms are in a charge group, rendering them fairly small. Looking in the TFE.itp, it's true, the whole molecule is in the same charged group 1 opls_160 1TFE CA3F 1 0.126 12.011 ; qtot 0.126 2 opls_161 1TFE CF3F 1 0.532 12.011 ; qtot 0.658 3 opls_162 1TFE OH3F 1 -0.63515.9994 ; qtot 0.023 4 opls_163 1TFE HO3F 1 0.429 1.008 ; qtot 0.452 5 opls_164 1TFE F13F 1 -0.20618.9984 ; qtot 0.246 6 opls_164 1TFE F23F 1 -0.20618.9984 ; qtot 0.04 7 opls_164 1TFE F33F 1 -0.20618.9984 ; qtot -0.166 8 opls_165 1TFE H13F 1 0.083 1.008 ; qtot -0.083 9 opls_165 1TFE H23F 1 0.083 1.008 ; qtot 0 *** Dra. Adriana D. Garro Química Medicinal Facultad de Química, Bioquímica y Farmacia Universidad Nacional de San Luis IMASL-CONICET San Luis, Argentina Tel..:+54 266 4424689 int 6153 e-mail...: adga...@unsl.edu.ar e-mail...: adrianagarr...@gmail.com ** -- == 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] Question
Hi, On Wed, Aug 12, 2015 at 9:47 PM Eric Smoll ericsm...@gmail.com wrote: Hello gromacs users, I am running a set of MD simulations where we are only interested in logging the coordinates and kinetic energy of a specific group in the system. I want to write the coordinates and energy of this group to file at every timestep. That's not an operation that mdrun supports. You can get all the coordinates and velocities, or a subset of the coordinates at a user-chosen precision, but that's all. Supplying an index file with the group of interest to grompp and specifying this group in the mdp file under energygrps doesn't seem to impact the edr file. The edr file still outputs the total system energy as a function of time. This is a limitation of the current GPU implementation - energygrps is not supported (and your md.log file will say this). Is there someway I can request that gromacs only compute the energy of one group in my system? Only when you postprocess the trajectory on just the CPU, e.g. with mdrun -rerun traj -nb cpu Will this result in a speedup? No. The bulk of the work is in the forces, so any savings from the energy calculation on only part of the interactions would be offset by the need to run a separate GPU kernel and do more book-keeping, so probably no gain. But as above, none of this is implemented. Are there other ways I can increase the speed of my simulation? My systems have 20,000-40,000 atoms with PME and 1.5 nm cutoffs. Are these simulations well suited for GPU acceleration or is this unlikely to produce a speedup? Speedup on a single GPU with a comparable CPU, yes. Mark Best, Eric -- 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] Change to umbrella sampling pull code
Thanks for clearing that up Justin, I’ve adjusted accordingly. All but one error remains: Pull group 1 'ZINC' has 1 atoms Pull group 2 'CARBONYL' has 1 atoms --- Program grompp, VERSION 5.0.5 Source code file: /home/columbus/chem_software/GROMACS/2015/gromacs-5.0.5/src/gromacs/gmxprep rocess/readpull.c, line: 377 Fatal error: Identical pull group indices in pull-coord1-groups For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- The entries in my index.ndx are: [ ZINC ] 5809 [ CARBONYL ] 6481 For the respective .mdp entries (pull code): ; Pull code pull= umbrella pull_geometry = distance pull_dim= Y Y Y pull_start = yes pull_ngroups= 2 pull_group1_name = ZINC pull_group2_name = CARBONYL pull_coord1_init = 0 pull_coord1_rate = 0 pull_coord1_k = 1000 pull_nstxout= 1000 ; every 2 ps pull_nstfout= 1000 ; every 2 ps On 12/08/2015 21:26, Justin Lemkul jalem...@vt.edu wrote: On 8/12/15 3:20 PM, Nash, Anthony wrote: Hi Mark, Thanks for the reply. Comparing the documentation between manual-4.5.6 (what I had previously been using) and manual-5.0.4: 4.5.6 has reference to pull_group0 as reference group, and in 5.0.4 there is no explicit mention (that I can see) to a reference group but there is one for the pull group (pull-group1-name). Right, because multiple reaction coordinates can now be simultaneously be restrained. There is no requirement for a single reference group. Any combination of groups can be used. Offhand, your settings are right except pull-ngroups is 2, as there are two groups. -Justin Thanks Anthony Dr Anthony Nash Department of Chemistry University College London On 12/08/2015 19:35, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, On Wed, Aug 12, 2015 at 6:20 PM Nash, Anthony a.n...@ucl.ac.uk wrote: Dear all, This is the first time I¹ve ran pull code (for umbrella sampling) since the change from Gromacs 4 to gromancs 5. I¹ve noticed some difference in the .mdp key-value parameters. Could I have a sanity check on the values below. I have no real idea, but you could start by comparing the respective documentation. If something's not clear, that's something to fix ;-) Also, given that I want a harmonic potential between the two groups, does it matter which index group is assigned to the respective Œpull-groupN-name¹ key? I doubt it, but if you want a definitive answer, make yourself a toy test case and see. Mark Note: my reaction coordinate was defined initially following the trajectory between two minima during a meta-dynamics MD simulation. That too was distance based. ;Pull code pull= umbrella pull-geometry = distance pull-dim= Y Y Y pull-start = yes pull-ngroups= 1 pull-group1-name = ZINC pull-group2-name = CARBONYL pull-coord1-init = 0 pull-coord1-rate = 0 pull-coord1-k = 1000 pull-nstxout= 1000 ; every 2 ps pull-nstfout= 1000 ; every 2 ps Many thanks Anthony -- 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. -- == 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
Re: [gmx-users] Change to umbrella sampling pull code
On 8/12/15 4:51 PM, Nash, Anthony wrote: Thanks for clearing that up Justin, I’ve adjusted accordingly. All but one error remains: Pull group 1 'ZINC' has 1 atoms Pull group 2 'CARBONYL' has 1 atoms --- Program grompp, VERSION 5.0.5 Source code file: /home/columbus/chem_software/GROMACS/2015/gromacs-5.0.5/src/gromacs/gmxprep rocess/readpull.c, line: 377 Fatal error: Identical pull group indices in pull-coord1-groups For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- You need: pull-coord1-groups = 1 2 otherwise the reaction coordinate is undefined, or otherwise defaults to the entire system, I can't remember which. -Justin The entries in my index.ndx are: [ ZINC ] 5809 [ CARBONYL ] 6481 For the respective .mdp entries (pull code): ; Pull code pull= umbrella pull_geometry = distance pull_dim= Y Y Y pull_start = yes pull_ngroups= 2 pull_group1_name = ZINC pull_group2_name = CARBONYL pull_coord1_init = 0 pull_coord1_rate = 0 pull_coord1_k = 1000 pull_nstxout= 1000 ; every 2 ps pull_nstfout= 1000 ; every 2 ps On 12/08/2015 21:26, Justin Lemkul jalem...@vt.edu wrote: On 8/12/15 3:20 PM, Nash, Anthony wrote: Hi Mark, Thanks for the reply. Comparing the documentation between manual-4.5.6 (what I had previously been using) and manual-5.0.4: 4.5.6 has reference to pull_group0 as reference group, and in 5.0.4 there is no explicit mention (that I can see) to a reference group but there is one for the pull group (pull-group1-name). Right, because multiple reaction coordinates can now be simultaneously be restrained. There is no requirement for a single reference group. Any combination of groups can be used. Offhand, your settings are right except pull-ngroups is 2, as there are two groups. -Justin Thanks Anthony Dr Anthony Nash Department of Chemistry University College London On 12/08/2015 19:35, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, On Wed, Aug 12, 2015 at 6:20 PM Nash, Anthony a.n...@ucl.ac.uk wrote: Dear all, This is the first time I¹ve ran pull code (for umbrella sampling) since the change from Gromacs 4 to gromancs 5. I¹ve noticed some difference in the .mdp key-value parameters. Could I have a sanity check on the values below. I have no real idea, but you could start by comparing the respective documentation. If something's not clear, that's something to fix ;-) Also, given that I want a harmonic potential between the two groups, does it matter which index group is assigned to the respective Œpull-groupN-name¹ key? I doubt it, but if you want a definitive answer, make yourself a toy test case and see. Mark Note: my reaction coordinate was defined initially following the trajectory between two minima during a meta-dynamics MD simulation. That too was distance based. ;Pull code pull= umbrella pull-geometry = distance pull-dim= Y Y Y pull-start = yes pull-ngroups= 1 pull-group1-name = ZINC pull-group2-name = CARBONYL pull-coord1-init = 0 pull-coord1-rate = 0 pull-coord1-k = 1000 pull-nstxout= 1000 ; every 2 ps pull-nstfout= 1000 ; every 2 ps Many thanks Anthony -- 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. -- == 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
Re: [gmx-users] Question
Mark and Justin, Thank you for the help. It is much appreciated. Is there a way to prevent the output of an .edr file altogether? Is there a way to prevent the output of a .trr file all together? Best, Eric On Wed, Aug 12, 2015 at 2:38 PM, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, On Wed, Aug 12, 2015 at 9:47 PM Eric Smoll ericsm...@gmail.com wrote: Hello gromacs users, I am running a set of MD simulations where we are only interested in logging the coordinates and kinetic energy of a specific group in the system. I want to write the coordinates and energy of this group to file at every timestep. That's not an operation that mdrun supports. You can get all the coordinates and velocities, or a subset of the coordinates at a user-chosen precision, but that's all. Supplying an index file with the group of interest to grompp and specifying this group in the mdp file under energygrps doesn't seem to impact the edr file. The edr file still outputs the total system energy as a function of time. This is a limitation of the current GPU implementation - energygrps is not supported (and your md.log file will say this). Is there someway I can request that gromacs only compute the energy of one group in my system? Only when you postprocess the trajectory on just the CPU, e.g. with mdrun -rerun traj -nb cpu Will this result in a speedup? No. The bulk of the work is in the forces, so any savings from the energy calculation on only part of the interactions would be offset by the need to run a separate GPU kernel and do more book-keeping, so probably no gain. But as above, none of this is implemented. Are there other ways I can increase the speed of my simulation? My systems have 20,000-40,000 atoms with PME and 1.5 nm cutoffs. Are these simulations well suited for GPU acceleration or is this unlikely to produce a speedup? Speedup on a single GPU with a comparable CPU, yes. Mark Best, Eric -- 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.
Re: [gmx-users] Change to umbrella sampling pull code
On 8/12/15 3:20 PM, Nash, Anthony wrote: Hi Mark, Thanks for the reply. Comparing the documentation between manual-4.5.6 (what I had previously been using) and manual-5.0.4: 4.5.6 has reference to pull_group0 as reference group, and in 5.0.4 there is no explicit mention (that I can see) to a reference group but there is one for the pull group (pull-group1-name). Right, because multiple reaction coordinates can now be simultaneously be restrained. There is no requirement for a single reference group. Any combination of groups can be used. Offhand, your settings are right except pull-ngroups is 2, as there are two groups. -Justin Thanks Anthony Dr Anthony Nash Department of Chemistry University College London On 12/08/2015 19:35, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, On Wed, Aug 12, 2015 at 6:20 PM Nash, Anthony a.n...@ucl.ac.uk wrote: Dear all, This is the first time I¹ve ran pull code (for umbrella sampling) since the change from Gromacs 4 to gromancs 5. I¹ve noticed some difference in the .mdp key-value parameters. Could I have a sanity check on the values below. I have no real idea, but you could start by comparing the respective documentation. If something's not clear, that's something to fix ;-) Also, given that I want a harmonic potential between the two groups, does it matter which index group is assigned to the respective Œpull-groupN-name¹ key? I doubt it, but if you want a definitive answer, make yourself a toy test case and see. Mark Note: my reaction coordinate was defined initially following the trajectory between two minima during a meta-dynamics MD simulation. That too was distance based. ;Pull code pull= umbrella pull-geometry = distance pull-dim= Y Y Y pull-start = yes pull-ngroups= 1 pull-group1-name = ZINC pull-group2-name = CARBONYL pull-coord1-init = 0 pull-coord1-rate = 0 pull-coord1-k = 1000 pull-nstxout= 1000 ; every 2 ps pull-nstfout= 1000 ; every 2 ps Many thanks Anthony -- 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. -- == 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] Charged group problem
On 8/12/15 9:30 AM, Adriana Garro wrote: Dear users, My system contains peptide + TFE + water in an octahedron box. I am using oplsaa.ff I am trying to do EM but running this command grompp -f em.mdp -c C22_TFE-W.gro -p topol.top -o em.tpr the next error message come up WARNING 1 [file em.mdp]: The sum of the two largest charge group radii (2.045171) is larger than rlist (1.00) I am afraid of changing the em.mdp parameters because as I understand these are the correct for my force field. I'd really appreciate suggestions! Assign smaller charge groups (fewer atoms), or use the Verlet cutoff scheme, for which charge groups are irrelevant (it's more accurate than the old group scheme, anyway). -Justin Thanks in advance Adriana here a part of the em.mdp file nstlist= 1 ns_type= grid rlist = 1.0 coulombtype= PME; Use particle-mesh ewald rcoulomb = 1.0 rvdw = 1.0 I read that large charge groups indicate that a fair number of atoms have been included in the same charge group. Usually only two or three atoms are in a charge group, rendering them fairly small. Looking in the TFE.itp, it's true, the whole molecule is in the same charged group 1 opls_160 1TFE CA3F 1 0.126 12.011 ; qtot 0.126 2 opls_161 1TFE CF3F 1 0.532 12.011 ; qtot 0.658 3 opls_162 1TFE OH3F 1 -0.63515.9994 ; qtot 0.023 4 opls_163 1TFE HO3F 1 0.429 1.008 ; qtot 0.452 5 opls_164 1TFE F13F 1 -0.20618.9984 ; qtot 0.246 6 opls_164 1TFE F23F 1 -0.20618.9984 ; qtot 0.04 7 opls_164 1TFE F33F 1 -0.20618.9984 ; qtot -0.166 8 opls_165 1TFE H13F 1 0.083 1.008 ; qtot -0.083 9 opls_165 1TFE H23F 1 0.083 1.008 ; qtot 0 *** Dra. Adriana D. Garro Química Medicinal Facultad de Química, Bioquímica y Farmacia Universidad Nacional de San Luis IMASL-CONICET San Luis, Argentina Tel..:+54 266 4424689 int 6153 e-mail...: adga...@unsl.edu.ar e-mail...: adrianagarr...@gmail.com ** -- == 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
On 8/12/15 5:12 PM, Eric Smoll wrote: Mark and Justin, Thank you for the help. It is much appreciated. Is there a way to prevent the output of an .edr file altogether? Is there a way to prevent the output of a .trr file all together? nstenergy = 0 nstxout = 0 nstvout = 0 nstfout = 0 Don't know how that's useful to you based on what you want to look at, but that's how you'd do it. -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
On 8/12/15 3:47 PM, Eric Smoll wrote: Hello gromacs users, I am running a set of MD simulations where we are only interested in logging the coordinates and kinetic energy of a specific group in the system. I want to write the coordinates and energy of this group to file at every timestep. Supplying an index file with the group of interest to grompp and specifying this group in the mdp file under energygrps doesn't seem to impact the edr file. The edr file still outputs the total system energy as a function of time. Is there someway I can request that gromacs only compute the energy of one group in my system? Will this result in a speedup? energygrps only decompose the short-range nonbonded interactions, nothing else. Are there other ways I can increase the speed of my simulation? My systems have 20,000-40,000 atoms with PME and 1.5 nm cutoffs. Are these simulations well suited for GPU acceleration or is this unlikely to produce a speedup? Depends on a lot of factors, but probably. That's a rather small system. Otherwise, if you just want to get the KE of some group, either: 1. Use gmx traj to calculate it from the velocities in the .trr (remember to account for any constraints that may be in use) 2. Extract the relevant group(s) of atoms from the .tpr and .trr (gmx convert-tpr and gmx trjconv, respectively) and use mdrun -rerun on the .trr -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] Distance restrain with dummy atom
On 8/12/15 10:24 AM, anu chandra wrote: Dear Justin, Thanks for the reply. As you suggested I have tried with flat-bottomed position restraint. Unfortunately, the water molecules were seen to be moving to vacuum that leads to membrane distortion. The methodology I adopted is as follows, 1. I done 5 ns equilibration of protein-membrane-water system. Later, I added ions to upper water layer. The box dimension of equilibrated system is 112.347 112.347 126.531 90.00 90.00 90.00. 2. Then I added a ~12nm vacuum slab along z-axis above and below the membrane using editconf command - editconf -f input.gro -o ouput.gro -c -box 11.2347 11.2347 37.9593 With walls or a flat-bottom restraint, additional vacuum space is unnecessary. Your distortion could be due to surface tension effects. 3. The 'output.gro' file from above step used for flat-bottomed position restraint simulation, where flat-bottomed position restraint applied on water and ions . The topology file looks as shown below, ** #include POT.itp #ifdef POSRES_ION ; Position restraint for potassium [ position_restraints ] ; i funct g r k 12 5 1 1000 #endif #include CL.itp #ifdef POSRES_ION ; Position restraint for chloride [ position_restraints ] ; i funct g r k 12 5 1 1000 #endif ; Include water topology #include charmm36-jun2015.ff/tip3p.itp #ifdef POSRES_WATER ; Position restraint for water [ position_restraints ] ; i funct g r k 12 5 1 1000 22 5 1 1000 32 5 1 1000 #endif * Here, I used layer geometry along z-axis and thickness of 1 nm. I have even tried with using thickness of half of the box length ( where the box length is excluded of vacuum slab) and also with restraining water oxygen alone. Unfortunately, all my trials has lead to water molecules flying to vacuum and membrane get distorted. Below is the mdp file is used for the simulation, Presumably because you're allowing them to. What you're saying is allow these atoms to move freely within 1 nm of where they are right now. That's not what you want. What you should do is construct a reference coordinate file (to be passed to grompp -r) that has the z-coordinate of any restrained atom set to a value of z/2 (easily done in a text editor). Then the restraint should be set to z/2 as well, which means those restrained species are allowed to move freely within half of the box. You should only have to apply the restraint to the ions, not the waters (assuming you eliminate the presumably unnecessary vacuum layer). -Justin ** define = -DPOSRES_ION -DPOSRES_WATER integrator = md dt = 0.001 nsteps = 1 nstlog = 1000 nstxout = 1000 nstvout = 1000 nstfout = 1000 nstcalcenergy = 100 nstenergy = 1000 ; cutoff-scheme = Verlet nstlist = 20 rlist = 1.2 coulombtype = pme rcoulomb= 1.2 vdwtype = Cut-off vdw-modifier= Force-switch rvdw_switch = 1.0 rvdw= 1.2 ; ewald-geometry = 3dc pbc = xyz ; tcoupl = V-rescale tc_grps = Protein POPC Cal_CL_SOL tau_t = 0.50.5 0.5 ref_t = 305.0305.0305.0 ; constraints = h-bonds constraint_algorithm= LINCS ; nstcomm = 100 comm_mode = linear comm_grps = Protein_POPC Cal_CL_SOL ; gen-vel = yes gen-temp= 305.0 gen-seed= -1 ; refcoord_scaling= com ** Can you please help me to figure out what is going wrong with the position restraint and simulation? Many thanks in advance Anu On Wed, Aug 12, 2015 at 12:44 AM, Justin Lemkul jalem...@vt.edu wrote: On 8/11/15 11:06 AM, anu chandra wrote: Dear Justin, Thanks for your quick reply. I am trying to run membrane protein simulation with slab geometry and EW3DC method (ewald-geometry = 3dc), due to ion asymmetry in the system. Following the article http://www.cell.com/biophysj/abstract/S0006-3495%2803%2974458-0?mobileUi=0 , I have set up my system with extended Z-dimension and used pbc = xyz. Unfortunately, when I carry out equilibration with EW3DC method and pbc=xyz, the membrane got distorted and become leaky. So, I trying to restraining water within a specific distance might help me to come out this
Re: [gmx-users] Local pressure of water
Please check the link below, http://repo.or.cz/w/gromacs.git/shortlog/refs/heads/release-4-5-localpressure On Tue, Aug 11, 2015 at 11:16 PM, 折晓会 shex...@hotmail.com wrote: Dear all,I am simulating polarizable water with Gromacs 5.0.5. I am wondering if it is possible to calculate the pressure profiles along z axis.I do not find corresponding programs from the manual. Instead, I find some discussions 4 years ago from the mailing list, but they do not make much sense to me. Any help will be appreciated!Best wishes, XiaohuiPh.D., University of Wisconsin-Madison -- 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] gmx cluster cut off
Dear all, I have done protein with three different inhibitor for 100ns simulation and would use the most populated structure for further analysis. What i wonder is how do i select the perfect cut off value to choose the most populated structure from 100ns? Is that following command can provide the a single structure to do my further analysis? gmx cluster -f prd_noPBC.xtc -s prd.tpr -o cluster.xpm -minstruct 10 -sz cluster-sizes.xvg -clid cluster-over-time.xvg -cl clusters.pdb -method gromos -dist rms-dist.xvg -noav -cutoff 0.25 I just confused which cut off value i should give to obtain the center most populated structure ? -- 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] Pdb file
L_BFGS On Tue, Aug 11, 2015 at 11:37 PM, Sunil Ghimire ghimiresuni...@gmail.com wrote: I created the pdb file by genconf but the system was not minimized, i got positive potential energy. What may be the problem? On 11 Aug 2015 19:38, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, gmx genconf on a small box with a single argon is a useful starting point. Mark On Tue, Aug 11, 2015 at 3:16 PM Sunil Ghimire ghimiresuni...@gmail.com wrote: How can i create the .pdb file for 1600 atoms of argon ? -- 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. -- 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] sample working DNA file?
Hi all, I have problems with a simple setup of DNA system. I try some programs to generate DNA pdb file. Some pdb output doesn't work. Some requires a lot of manual edits. I finally got a pdb file working but I still have some problems with long bonds. Does anybody have a sample working DNA pdb file and could share with me? Thanks Toan -- 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] Change to umbrella sampling pull code
Dear all, This is the first time I¹ve ran pull code (for umbrella sampling) since the change from Gromacs 4 to gromancs 5. I¹ve noticed some difference in the .mdp key-value parameters. Could I have a sanity check on the values below. Also, given that I want a harmonic potential between the two groups, does it matter which index group is assigned to the respective Œpull-groupN-name¹ key? Note: my reaction coordinate was defined initially following the trajectory between two minima during a meta-dynamics MD simulation. That too was distance based. ;Pull code pull= umbrella pull-geometry = distance pull-dim= Y Y Y pull-start = yes pull-ngroups= 1 pull-group1-name = ZINC pull-group2-name = CARBONYL pull-coord1-init = 0 pull-coord1-rate = 0 pull-coord1-k = 1000 pull-nstxout= 1000 ; every 2 ps pull-nstfout= 1000 ; every 2 ps Many thanks Anthony -- 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] bonded parameter
Hi ?Which step of simulation the bonded parameters of available in a force field will be used -- 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] Charmm 36 parameter file for gromacs
Dear Dr Justin and Gromacs User, As I mentioned in the previous email , I download the parameter from this website which was build for all-atom simulation ( http://mmkluster.fos.su.se/slipids/Downloads.html ). I attached the file below . I have a confusion with Tielema's website. I use this for run membrane protein simulations and it work well, no errors like the topology which was embedded in charmm36 force field for with Gromacs format. I just want to ask why I got many error when I use the topology which was embedded in charmm36 force field for with Gromacs format? Some suggestion to me please. Dear Dr. Justin Thank you so much for your suggestion. I will try with CHARMM-GUI. Best regards, Tuong Vy 2015-08-12 21:19 GMT+09:00 Vy Phan phanvy120...@gmail.com: Dear Dr Justin and Gromacs User, As I mentioned in the previous email , I download the parameter from this website which was build for all-atom simulation ( http://mmkluster.fos.su.se/slipids/Downloads.html ). I attached the file below . I have a confusion with Tielema's website. I use this for run membrane protein simulations and it work well, no errors like the topology which was embedded in charmm36 force field for with Gromacs format. I just want to ask why I got many error when I use the topology which was embedded in charmm36 force field for with Gromacs format? Some suggestion to me please. Dear Dr. Justin Thank you so much for your suggestion. I will try with CHARMM-GUI. Best regards, Tuong Vy 2015-08-12 20:32 GMT+09:00 Justin Lemkul jalem...@vt.edu: On 8/11/15 10:15 PM, Vy Phan wrote: Dear Dr. Justin and Gromacs User, Thank you so much for your helps. When I use charmm36 ff to generate the topology for lipid (DOPC). I got many warning Warning :Long bond And after get the topology, the total charge is very high (+888 e for DOPC bilayer have 516 molecular). When I used grompp to generate the .tpr file, I got the many error like this : Error 3379 [file topol_Other_chain_D.itp, line 198252] No defaut U-B types ... Error 2379 [file topol_Other_chain_D.itp, line 98252] No default Proper Dih.type What can I do to modified the topology to get the correct charge and fix the error ? I download dopc.itp from Tieleman's website. I run simulation and all things look fine. People have experiences, please tell me the difference of this topology and the one on the charmm36 force field. The files Tieleman provides are united-atom structures that may use a different naming convention. They won't have H atoms on the aliphatic groups and there is no .hdb entry for DOPC. The ridiculous net charge you got for DOPC (which is neutral!) should be an indicator that whatever topology you built is utter nonsense. There should also be no warnings about missing parameters, so this is further evidence that the topology is wrong and the things look fine assertion seems totally unfounded to me. If you want to simulate a simple membrane, use CHARMM-GUI to build it. It will be 100% CHARMM compliant and we give you all the necessary input files. -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] Charmm 36 parameter file for gromacs
On 8/11/15 10:15 PM, Vy Phan wrote: Dear Dr. Justin and Gromacs User, Thank you so much for your helps. When I use charmm36 ff to generate the topology for lipid (DOPC). I got many warning Warning :Long bond And after get the topology, the total charge is very high (+888 e for DOPC bilayer have 516 molecular). When I used grompp to generate the .tpr file, I got the many error like this : Error 3379 [file topol_Other_chain_D.itp, line 198252] No defaut U-B types ... Error 2379 [file topol_Other_chain_D.itp, line 98252] No default Proper Dih.type What can I do to modified the topology to get the correct charge and fix the error ? I download dopc.itp from Tieleman's website. I run simulation and all things look fine. People have experiences, please tell me the difference of this topology and the one on the charmm36 force field. The files Tieleman provides are united-atom structures that may use a different naming convention. They won't have H atoms on the aliphatic groups and there is no .hdb entry for DOPC. The ridiculous net charge you got for DOPC (which is neutral!) should be an indicator that whatever topology you built is utter nonsense. There should also be no warnings about missing parameters, so this is further evidence that the topology is wrong and the things look fine assertion seems totally unfounded to me. If you want to simulate a simple membrane, use CHARMM-GUI to build it. It will be 100% CHARMM compliant and we give you all the necessary input files. -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] sample working DNA file?
On 8/12/15 6:07 AM, toannt wrote: Hi all, I have problems with a simple setup of DNA system. I try some programs to generate DNA pdb file. Some pdb output doesn't work. Some requires a lot of manual edits. I finally got a pdb file working but I still have some problems with long bonds. Does anybody have a sample working DNA pdb file and could share with me? DNA structures unfortunately do not always have the same level of standardized nomenclature as proteins, so some manual editing or use of .r2b files is needed, especially as naming also varies among force fields. A sort of bulletproof DNA structure is PDB 1BNA (or really anything else that isn't missing any atoms). -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] Charmm 36 parameter file for gromacs
Dear Dr. Justin I got your means and it is very helpful for me. Thank you so much :) Sincerely, Tuong Vy 2015-08-12 21:23 GMT+09:00 Justin Lemkul jalem...@vt.edu: On 8/12/15 8:20 AM, Vy Phan wrote: Dear Dr Justin and Gromacs User, As I mentioned in the previous email , I download the parameter from this website which was build for all-atom simulation ( http://mmkluster.fos.su.se/slipids/Downloads.html ). I attached the file The list does not accept attachments, not is it necessary. below . I have a confusion with Tielema's website. I use this for run membrane protein simulations and it work well, no errors like the topology which was embedded in charmm36 force field for with Gromacs format. Previous success with a different force field has no bearing on future success with a different model that uses a different convention (all-atom vs. united-atom). I just want to ask why I got many error when I use the topology which was embedded in charmm36 force field for with Gromacs format? Some suggestion to me please. As I said before, you have serious problems with whatever topology you managed to generate. A charge of +888 on a 516-lipid DOPC (which is neutral) is total nonsense, so you certainly have missing or incorrect atoms that you've bypassed with pdb2gmx options or something else. Whatever that topology has in it is certainly wrong and should not be used. -Justin Dear Dr. Justin Thank you so much for your suggestion. I will try with CHARMM-GUI. Best regards, Tuong Vy 2015-08-12 21:19 GMT+09:00 Vy Phan phanvy120...@gmail.com: Dear Dr Justin and Gromacs User, As I mentioned in the previous email , I download the parameter from this website which was build for all-atom simulation ( http://mmkluster.fos.su.se/slipids/Downloads.html ). I attached the file below . I have a confusion with Tielema's website. I use this for run membrane protein simulations and it work well, no errors like the topology which was embedded in charmm36 force field for with Gromacs format. I just want to ask why I got many error when I use the topology which was embedded in charmm36 force field for with Gromacs format? Some suggestion to me please. Dear Dr. Justin Thank you so much for your suggestion. I will try with CHARMM-GUI. Best regards, Tuong Vy 2015-08-12 20:32 GMT+09:00 Justin Lemkul jalem...@vt.edu: On 8/11/15 10:15 PM, Vy Phan wrote: Dear Dr. Justin and Gromacs User, Thank you so much for your helps. When I use charmm36 ff to generate the topology for lipid (DOPC). I got many warning Warning :Long bond And after get the topology, the total charge is very high (+888 e for DOPC bilayer have 516 molecular). When I used grompp to generate the .tpr file, I got the many error like this : Error 3379 [file topol_Other_chain_D.itp, line 198252] No defaut U-B types ... Error 2379 [file topol_Other_chain_D.itp, line 98252] No default Proper Dih.type What can I do to modified the topology to get the correct charge and fix the error ? I download dopc.itp from Tieleman's website. I run simulation and all things look fine. People have experiences, please tell me the difference of this topology and the one on the charmm36 force field. The files Tieleman provides are united-atom structures that may use a different naming convention. They won't have H atoms on the aliphatic groups and there is no .hdb entry for DOPC. The ridiculous net charge you got for DOPC (which is neutral!) should be an indicator that whatever topology you built is utter nonsense. There should also be no warnings about missing parameters, so this is further evidence that the topology is wrong and the things look fine assertion seems totally unfounded to me. If you want to simulate a simple membrane, use CHARMM-GUI to build it. It will be 100% CHARMM compliant and we give you all the necessary input files. -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
Re: [gmx-users] Charmm 36 parameter file for gromacs
On 8/12/15 8:20 AM, Vy Phan wrote: Dear Dr Justin and Gromacs User, As I mentioned in the previous email , I download the parameter from this website which was build for all-atom simulation ( http://mmkluster.fos.su.se/slipids/Downloads.html ). I attached the file The list does not accept attachments, not is it necessary. below . I have a confusion with Tielema's website. I use this for run membrane protein simulations and it work well, no errors like the topology which was embedded in charmm36 force field for with Gromacs format. Previous success with a different force field has no bearing on future success with a different model that uses a different convention (all-atom vs. united-atom). I just want to ask why I got many error when I use the topology which was embedded in charmm36 force field for with Gromacs format? Some suggestion to me please. As I said before, you have serious problems with whatever topology you managed to generate. A charge of +888 on a 516-lipid DOPC (which is neutral) is total nonsense, so you certainly have missing or incorrect atoms that you've bypassed with pdb2gmx options or something else. Whatever that topology has in it is certainly wrong and should not be used. -Justin Dear Dr. Justin Thank you so much for your suggestion. I will try with CHARMM-GUI. Best regards, Tuong Vy 2015-08-12 21:19 GMT+09:00 Vy Phan phanvy120...@gmail.com: Dear Dr Justin and Gromacs User, As I mentioned in the previous email , I download the parameter from this website which was build for all-atom simulation ( http://mmkluster.fos.su.se/slipids/Downloads.html ). I attached the file below . I have a confusion with Tielema's website. I use this for run membrane protein simulations and it work well, no errors like the topology which was embedded in charmm36 force field for with Gromacs format. I just want to ask why I got many error when I use the topology which was embedded in charmm36 force field for with Gromacs format? Some suggestion to me please. Dear Dr. Justin Thank you so much for your suggestion. I will try with CHARMM-GUI. Best regards, Tuong Vy 2015-08-12 20:32 GMT+09:00 Justin Lemkul jalem...@vt.edu: On 8/11/15 10:15 PM, Vy Phan wrote: Dear Dr. Justin and Gromacs User, Thank you so much for your helps. When I use charmm36 ff to generate the topology for lipid (DOPC). I got many warning Warning :Long bond And after get the topology, the total charge is very high (+888 e for DOPC bilayer have 516 molecular). When I used grompp to generate the .tpr file, I got the many error like this : Error 3379 [file topol_Other_chain_D.itp, line 198252] No defaut U-B types ... Error 2379 [file topol_Other_chain_D.itp, line 98252] No default Proper Dih.type What can I do to modified the topology to get the correct charge and fix the error ? I download dopc.itp from Tieleman's website. I run simulation and all things look fine. People have experiences, please tell me the difference of this topology and the one on the charmm36 force field. The files Tieleman provides are united-atom structures that may use a different naming convention. They won't have H atoms on the aliphatic groups and there is no .hdb entry for DOPC. The ridiculous net charge you got for DOPC (which is neutral!) should be an indicator that whatever topology you built is utter nonsense. There should also be no warnings about missing parameters, so this is further evidence that the topology is wrong and the things look fine assertion seems totally unfounded to me. If you want to simulate a simple membrane, use CHARMM-GUI to build it. It will be 100% CHARMM compliant and we give you all the necessary input files. -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
[gmx-users] Charged group problem
Dear users, My system contains peptide + TFE + water in an octahedron box. I am using oplsaa.ff I am trying to do EM but running this command grompp -f em.mdp -c C22_TFE-W.gro -p topol.top -o em.tpr the next error message come up WARNING 1 [file em.mdp]: The sum of the two largest charge group radii (2.045171) is larger than rlist (1.00) I am afraid of changing the em.mdp parameters because as I understand these are the correct for my force field. I'd really appreciate suggestions! Thanks in advance Adriana here a part of the em.mdp file nstlist= 1 ns_type= grid rlist = 1.0 coulombtype= PME; Use particle-mesh ewald rcoulomb = 1.0 rvdw = 1.0 I read that large charge groups indicate that a fair number of atoms have been included in the same charge group. Usually only two or three atoms are in a charge group, rendering them fairly small. Looking in the TFE.itp, it's true, the whole molecule is in the same charged group 1 opls_160 1TFE CA3F 1 0.126 12.011 ; qtot 0.126 2 opls_161 1TFE CF3F 1 0.532 12.011 ; qtot 0.658 3 opls_162 1TFE OH3F 1 -0.63515.9994 ; qtot 0.023 4 opls_163 1TFE HO3F 1 0.429 1.008 ; qtot 0.452 5 opls_164 1TFE F13F 1 -0.20618.9984 ; qtot 0.246 6 opls_164 1TFE F23F 1 -0.20618.9984 ; qtot 0.04 7 opls_164 1TFE F33F 1 -0.20618.9984 ; qtot -0.166 8 opls_165 1TFE H13F 1 0.083 1.008 ; qtot -0.083 9 opls_165 1TFE H23F 1 0.083 1.008 ; qtot 0 *** Dra. Adriana D. Garro Química Medicinal Facultad de Química, Bioquímica y Farmacia Universidad Nacional de San Luis IMASL-CONICET San Luis, Argentina Tel..:+54 266 4424689 int 6153 e-mail...: adga...@unsl.edu.ar e-mail...: adrianagarr...@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.
[gmx-users] Force constant
Dear all, I have to write the .itp file for my molecule, and I have problem with finding the correct value for force constants. Is it possible to calculate bond/angle force constant from ab initio calculation? Thank you in advance Mehrnoosh -- 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] bonded parameter
Hi, Either your topology doesn't use those parameters, or the interactions that use them were converted to constraints by the settings in your .mdp file. (By the way, it is better to talk about a stage of an MD workflow, as step can be misunderstood to mean an integration step.) Mark On Wed, Aug 12, 2015 at 7:57 PM حسن هاشم زاده hashemzadehas...@gmail.com wrote: but I delete bonded parameter from my force field in spite of this topology file was created and all step is runing without any error 2015-08-12 21:56 GMT+04:30 Maryam Kowsar maryam.kow...@gmail.com: Hi Hassan, For making a topology(.top) file all parameters of your forcefield is needed. On Wed, Aug 12, 2015 at 9:37 PM, حسن هاشم زاده hashemzadehas...@gmail.com wrote: Hi ?Which step of simulation the bonded parameters of available in a force field will be used -- 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. -- 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] bonded parameter
Yes, but only you know which! Mark On Wed, Aug 12, 2015 at 8:45 PM حسن هاشم زاده hashemzadehas...@gmail.com wrote: this means that bonded parameter not necessary for my work or that my work is wrong 2015-08-12 22:53 GMT+04:30 Mark Abraham mark.j.abra...@gmail.com: Hi, Either your topology doesn't use those parameters, or the interactions that use them were converted to constraints by the settings in your .mdp file. (By the way, it is better to talk about a stage of an MD workflow, as step can be misunderstood to mean an integration step.) Mark On Wed, Aug 12, 2015 at 7:57 PM حسن هاشم زاده hashemzadehas...@gmail.com wrote: but I delete bonded parameter from my force field in spite of this topology file was created and all step is runing without any error 2015-08-12 21:56 GMT+04:30 Maryam Kowsar maryam.kow...@gmail.com: Hi Hassan, For making a topology(.top) file all parameters of your forcefield is needed. On Wed, Aug 12, 2015 at 9:37 PM, حسن هاشم زاده hashemzadehas...@gmail.com wrote: Hi ?Which step of simulation the bonded parameters of available in a force field will be used -- 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. -- 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.
Re: [gmx-users] Change to umbrella sampling pull code
Hi Mark, Thanks for the reply. Comparing the documentation between manual-4.5.6 (what I had previously been using) and manual-5.0.4: 4.5.6 has reference to pull_group0 as reference group, and in 5.0.4 there is no explicit mention (that I can see) to a reference group but there is one for the pull group (pull-group1-name). Thanks Anthony Dr Anthony Nash Department of Chemistry University College London On 12/08/2015 19:35, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, On Wed, Aug 12, 2015 at 6:20 PM Nash, Anthony a.n...@ucl.ac.uk wrote: Dear all, This is the first time I¹ve ran pull code (for umbrella sampling) since the change from Gromacs 4 to gromancs 5. I¹ve noticed some difference in the .mdp key-value parameters. Could I have a sanity check on the values below. I have no real idea, but you could start by comparing the respective documentation. If something's not clear, that's something to fix ;-) Also, given that I want a harmonic potential between the two groups, does it matter which index group is assigned to the respective Œpull-groupN-name¹ key? I doubt it, but if you want a definitive answer, make yourself a toy test case and see. Mark Note: my reaction coordinate was defined initially following the trajectory between two minima during a meta-dynamics MD simulation. That too was distance based. ;Pull code pull= umbrella pull-geometry = distance pull-dim= Y Y Y pull-start = yes pull-ngroups= 1 pull-group1-name = ZINC pull-group2-name = CARBONYL pull-coord1-init = 0 pull-coord1-rate = 0 pull-coord1-k = 1000 pull-nstxout= 1000 ; every 2 ps pull-nstfout= 1000 ; every 2 ps Many thanks Anthony -- 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.
Re: [gmx-users] bonded parameter
Hi, I mean that I can't possibly tell what your problem is, because you've shared zero information. You probably want to look at the PDF reference manual for the documentation of the constraints .mdp option. Whether that matters depends what you've chosen, but I don't know that. See http://www.gromacs.org/Support for clues on how you might succeed at getting help from people. Mark On Wed, Aug 12, 2015 at 8:55 PM Mark Abraham mark.j.abra...@gmail.com wrote: Yes, but only you know which! Mark On Wed, Aug 12, 2015 at 8:45 PM حسن هاشم زاده hashemzadehas...@gmail.com wrote: this means that bonded parameter not necessary for my work or that my work is wrong 2015-08-12 22:53 GMT+04:30 Mark Abraham mark.j.abra...@gmail.com: Hi, Either your topology doesn't use those parameters, or the interactions that use them were converted to constraints by the settings in your .mdp file. (By the way, it is better to talk about a stage of an MD workflow, as step can be misunderstood to mean an integration step.) Mark On Wed, Aug 12, 2015 at 7:57 PM حسن هاشم زاده hashemzadehas...@gmail.com wrote: but I delete bonded parameter from my force field in spite of this topology file was created and all step is runing without any error 2015-08-12 21:56 GMT+04:30 Maryam Kowsar maryam.kow...@gmail.com: Hi Hassan, For making a topology(.top) file all parameters of your forcefield is needed. On Wed, Aug 12, 2015 at 9:37 PM, حسن هاشم زاده hashemzadehas...@gmail.com wrote: Hi ?Which step of simulation the bonded parameters of available in a force field will be used -- 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. -- 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.
Re: [gmx-users] Pdb file
Hello, I guess it is not unusual for gaseous systems to have positive energy. I hope that the Fmax criteria is satisfied. Sujith. On Wed, Aug 12, 2015 at 10:30 AM, Sunil Ghimire ghimiresuni...@gmail.com wrote: I mean potential energy of system (1600 argon atoms) is positive after energy mininization . On 12 Aug 2015 16:58, Vitaly V. Chaban vvcha...@gmail.com wrote: L_BFGS On Tue, Aug 11, 2015 at 11:37 PM, Sunil Ghimire ghimiresuni...@gmail.com wrote: I created the pdb file by genconf but the system was not minimized, i got positive potential energy. What may be the problem? On 11 Aug 2015 19:38, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, gmx genconf on a small box with a single argon is a useful starting point. Mark On Tue, Aug 11, 2015 at 3:16 PM Sunil Ghimire ghimiresuni...@gmail.com wrote: How can i create the .pdb file for 1600 atoms of argon ? -- 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. -- 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.
Re: [gmx-users] Change to umbrella sampling pull code
Hi, On Wed, Aug 12, 2015 at 6:20 PM Nash, Anthony a.n...@ucl.ac.uk wrote: Dear all, This is the first time I¹ve ran pull code (for umbrella sampling) since the change from Gromacs 4 to gromancs 5. I¹ve noticed some difference in the .mdp key-value parameters. Could I have a sanity check on the values below. I have no real idea, but you could start by comparing the respective documentation. If something's not clear, that's something to fix ;-) Also, given that I want a harmonic potential between the two groups, does it matter which index group is assigned to the respective Œpull-groupN-name¹ key? I doubt it, but if you want a definitive answer, make yourself a toy test case and see. Mark Note: my reaction coordinate was defined initially following the trajectory between two minima during a meta-dynamics MD simulation. That too was distance based. ;Pull code pull= umbrella pull-geometry = distance pull-dim= Y Y Y pull-start = yes pull-ngroups= 1 pull-group1-name = ZINC pull-group2-name = CARBONYL pull-coord1-init = 0 pull-coord1-rate = 0 pull-coord1-k = 1000 pull-nstxout= 1000 ; every 2 ps pull-nstfout= 1000 ; every 2 ps Many thanks Anthony -- 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] bonded parameter
this means that bonded parameter not necessary for my work or that my work is wrong 2015-08-12 22:53 GMT+04:30 Mark Abraham mark.j.abra...@gmail.com: Hi, Either your topology doesn't use those parameters, or the interactions that use them were converted to constraints by the settings in your .mdp file. (By the way, it is better to talk about a stage of an MD workflow, as step can be misunderstood to mean an integration step.) Mark On Wed, Aug 12, 2015 at 7:57 PM حسن هاشم زاده hashemzadehas...@gmail.com wrote: but I delete bonded parameter from my force field in spite of this topology file was created and all step is runing without any error 2015-08-12 21:56 GMT+04:30 Maryam Kowsar maryam.kow...@gmail.com: Hi Hassan, For making a topology(.top) file all parameters of your forcefield is needed. On Wed, Aug 12, 2015 at 9:37 PM, حسن هاشم زاده hashemzadehas...@gmail.com wrote: Hi ?Which step of simulation the bonded parameters of available in a force field will be used -- 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. -- 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] bonded parameter
Hi Hassan, For making a topology(.top) file all parameters of your forcefield is needed. On Wed, Aug 12, 2015 at 9:37 PM, حسن هاشم زاده hashemzadehas...@gmail.com wrote: Hi ?Which step of simulation the bonded parameters of available in a force field will be used -- 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] Force constant
Hi, To which I would also suggest adding checks of any available experimental quantities (e.g. density, heat of vaporization) and considering carefully following the techniques used in parametrizing the parent force field. Mark On Wed, Aug 12, 2015 at 5:24 PM André Farias de Moura mo...@ufscar.br wrote: sure, it can be done (not published yet, but we did it for a small molecule recently - CH2I2): (1) chose an appropriate level of theory and basis set, perform geometry optimization and frequency calculation (mind that each combination of level of theory and basis set have its own scaling factor to correct systematic errors in frequencies arising from the harmonic oscillator approximation) (2) you should guess an initial value for the missing force constants, then you should perform a single molecule, vacuum simulation of your target molecule (you need to remove PBC, angular and linear momenta an you'll probably need double precision for that, along with a short time step, maybe below 1 fs). How long the simulation should be depends on the lowest frequencies you might be interested in. (3) calculate the velocity autocorrelation function and take its Fourier transform, then compare it with the quantum chemical result. (4) adjust the force constant and repeat steps 2-3 until convergence is achieved (MM IR spectrum matches QM IR spectrum satisfactorily) On Wed, Aug 12, 2015 at 11:11 AM, Mehrnoosh Hazrati mehrnoosh.hazr...@modares.ac.ir wrote: Dear all, I have to write the .itp file for my molecule, and I have problem with finding the correct value for force constants. Is it possible to calculate bond/angle force constant from ab initio calculation? Thank you in advance Mehrnoosh -- 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. -- _ Prof. Dr. André Farias de Moura Department of Chemistry Federal University of São Carlos São Carlos - Brazil phone: +55-16-3351-8090 -- 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] bonded parameter
but I delete bonded parameter from my force field in spite of this topology file was created and all step is runing without any error 2015-08-12 21:56 GMT+04:30 Maryam Kowsar maryam.kow...@gmail.com: Hi Hassan, For making a topology(.top) file all parameters of your forcefield is needed. On Wed, Aug 12, 2015 at 9:37 PM, حسن هاشم زاده hashemzadehas...@gmail.com wrote: Hi ?Which step of simulation the bonded parameters of available in a force field will be used -- 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] Question
Hello gromacs users, I am running a set of MD simulations where we are only interested in logging the coordinates and kinetic energy of a specific group in the system. I want to write the coordinates and energy of this group to file at every timestep. Supplying an index file with the group of interest to grompp and specifying this group in the mdp file under energygrps doesn't seem to impact the edr file. The edr file still outputs the total system energy as a function of time. Is there someway I can request that gromacs only compute the energy of one group in my system? Will this result in a speedup? Are there other ways I can increase the speed of my simulation? My systems have 20,000-40,000 atoms with PME and 1.5 nm cutoffs. Are these simulations well suited for GPU acceleration or is this unlikely to produce a speedup? Best, Eric -- 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.
