[gmx-users] Dihedral restraint for entire super structure
Hi I am trying to model a MOF solvation in water. I would like to treat MOF as a rigid framework. I have non-bonded parameters of MOF available from literature and bonded parameters from UFF (calculated using Avogadro) I mentioned bond and angle constraints in my mdp files and I would like to specify dihedral restraints so as to maintain MOF rigid. How can I restrain all the dihedrals of MOF in dihedral restrain, for a single unit cell I have about 1000 dihedrals. Thank You With Regards Nagasree Garapati Research Assistant Professor Dept of Chemical and Biomedical Engineering West Virginia University PO Box 6102 Morgantown, WV 26506-6102 304 293-5028(O) 304 276-3674(M) -- 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] zig-zag stacking
Thank You Dan and Lakshman I will try using gmx editconf and try to translate and see if I could get the arrangement. I am trying to create a super cell of 7x7x1 size and each unit cell has about 276 atoms, so I was trying to find out if there is any other simpler utility/program like genconf which can do zigzag stacking for such a big super cell. Lakshman I am not sure if I followed your suggestion, how can we translate only one molecule in a box using editconf? With Regards Nagasree Garapati Research Assistant Professor Dept of Chemical and Biomedical Engineering West Virginia University PO Box 6102 Morgantown, WV 26506-6102 304 293-5028(O) 304 276-3674(M) From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of gromacs.org_gmx-users-requ...@maillist.sys.kth.se Sent: Tuesday, July 31, 2018 8:41 PM To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: gromacs.org_gmx-users Digest, Vol 172, Issue 1 Send gromacs.org_gmx-users mailing list submissions to gromacs.org_gmx-users@maillist.sys.kth.se To subscribe or unsubscribe via the World Wide Web, visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or, via email, send a message with subject or body 'help' to gromacs.org_gmx-users-requ...@maillist.sys.kth.se You can reach the person managing the list at gromacs.org_gmx-users-ow...@maillist.sys.kth.se When replying, please edit your Subject line so it is more specific than "Re: Contents of gromacs.org_gmx-users digest..." Today's Topics: 1. Re: non-global thermostatting (Justin Lemkul) 2. potential energy (Mahboobeh Eslami) 3. Re: zig-zag stacking (Dan Gil) 4. Re: ndx file with frames (Dan Gil) 5. Re: zig-zag stacking (Lakshman Ji Verma) 6. Re: non-global thermostatting (Alex) -- Message: 1 Date: Tue, 31 Jul 2018 16:22:29 -0400 From: Justin Lemkul To: gmx-us...@gromacs.org Subject: Re: [gmx-users] non-global thermostatting Message-ID: Content-Type: text/plain; charset=utf-8; format=flowed On 7/31/18 4:13 PM, Alex wrote: >> >> No, as all atoms have to be specified within some group. But you can >> disable thermostatting on a given group by setting tau_t = -1. >> >> >> Not sure I understand... I have several groups (say, GRP1, GRP2, etc) and > the only one I want to be thermostatted is SOL. Does that mean that I > should have something like: > > tc-grps = SOL GRP1 GRP2 ... > tau_t = 0.1 -1 -1 ... > > ? Yes. > What happens if instead I happen to have only the original statement? You'll get a fatal error from grompp. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- Message: 2 Date: Tue, 31 Jul 2018 20:34:14 + (UTC) From: Mahboobeh Eslami To: Discussion List for GROMACS Users Subject: [gmx-users] potential energy Message-ID: <806715418.48695.1533069254...@mail.yahoo.com> Content-Type: text/plain; charset=UTF-8 Hi all GMX usersI did MD simulation under NPT ensembel. I evaluated potential energy during?energy minimization, equilibration, and productionMD steps.? The plot of? potential energy?indicates the nice, steady convergence of potentialenergy during energy minimization step.?The first equilibration phase has been conductedunder an NVT ensemble. The temperature of the system quickly has been reachedthe target value (300 K) during this step. The potential energy has been alsoincreased quickly and then reached to steady state. Is the system?in its minimum potential energy in this step??The potential energy has been almost constantduring the second equilibration phase and production MD.?These steps performed under NPT ensemble. Did MD sinualtion perform?appropriately? please guide me.Thanks a lot? -- Message: 3 Date: Tue, 31 Jul 2018 19:38:41 -0400 From: Dan Gil To: gmx-us...@gromacs.org Subject: Re: [gmx-users] zig-zag stacking Message-ID: Content-Type: text/plain; charset="UTF-8" Hi, I haven't tried it, but I wonder if the gmx editconf utility can be used to translate groups of atoms, where the group is defined with an index file (make_ndx). Dan On Tue, Jul 31, 2018 at 1:21 PM, Nagasree Garapati < nagasree.garap...@mail.wvu.edu> wrote: > Hi All > > > I am trying to look at the pore space availability and property > differences between supercells created by stacking unitcells on top of each > other and by zigzag stacking. > > In Gromacs genconf can be used to create a super cell by sta
[gmx-users] zig-zag stacking
Hi All I am trying to look at the pore space availability and property differences between supercells created by stacking unitcells on top of each other and by zigzag stacking. In Gromacs genconf can be used to create a super cell by stacking unit cells on top of each other, is there a way to create zig zag stacking? Thank You With Regards Nagasree Garapati Research Assistant Professor Dept of Chemical and Biomedical Engineering West Virginia University PO Box 6102 Morgantown, WV 26506-6102 304 293-5028(O) 304 276-3674(M) -- 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] Energy minimization of solvated MOFs.
Hi I am trying to run some simulations on Metal-Organic frameworks like ZIF-8. I have obtained both structure file (from CCDC) and forcefield data from literature and I was able to successfully run energy minimization, and equilibirum MD (NVT and NPT) simulations on the crystal structure of MOF. But when I tried to perform energy minimization for a system of MOF in water (by putting MOF in a box and solvating using gmx solvate), I am getting following message and forces are very high on water molecules. I am not how to overcome this problem, any thoughts are appreciated. "Energy minimization has stopped, but the forces have not converged to the requested precision Fmax < 5 (which may not be possible for your system). It stopped because the algorithm tried to make a new step whose size was too small, or there was no change in the energy since last step. Either way, we regard the minimization as converged to within the available machine precision, given your starting configuration and EM parameters. writing lowest energy coordinates. Steepest Descents converged to machine precision in 95 steps, but did not reach the requested Fmax < 5. Potential Energy = -3.38556029741624e+13 Maximum force = 2.45386477264935e+25 on atom 306 Norm of force = 1.49337454338593e+24" Thank You With Regards Nagasree Garapati Research Assistant Professor Dept of Chemical and Biomedical Engineering West Virginia University PO Box 6102 Morgantown, WV 26506-6102 304 293-5028(O) 304 276-3674(M) -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Error in NPT simulation
Dear all I am getting following error while running NPT simulation. I did energy minimization and NVT simulations, which ran successfully but when I proceed to NPT simulation, I am getting below error. Step 142, time 0.284 (ps) LINCS WARNING relative constraint deviation after LINCS: rms -nan, max 0.003869 (between atoms 33 and 76) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length Segmentation fault (core dumped) Not sure, what could be the reason for error. Any thoughts ? With Regards Nagasree Garapati Research Assistant Professor Dept of Chemical and Biomedical Engineering West Virginia University PO Box 6102 Morgantown, WV 26506-6102 304 293-5028(O) 304 276-3674(M) -- 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] Fw: Geometry Optimization for Metal organic Frame works
Thank You Micholas I have created the topology files using initial input file in OBGMX and it shows that there are 20 unique bond terms, out of which there are 3 bonds between the metal ion and the N2 in linker. However, when I tried to create topolgies using the optimized final output (final.gro) file in OBGMX, nothing is created I have empty files for both .top and .itp files. I believe there is something wrong with the topology files, but I am not able to figure out where is the mistake. Any suggestions ? Thank You With Regards Nagasree Garapati Research Assistant Professor Dept of Chemical and Biomedical Engineering West Virginia University PO Box 6102 Morgantown, WV 26506-6102 304 293-5028<tel:304%20293-5028>(O) 304 276-3674(M) -- 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] Geometry Optimization for Metal organic Frame works
Hi All I am new user for GROMACS and I am trying model Metal Organic Frame works (MOFs) I have crystal structure (CIF) file downloaded from Cambridge Crystallographic Data Center (CCDC) and used OBGMX tool to develop force field parameters and used following minim.mdp file for optimization. But after optimization, when I visualize the output .gro file I see that all the bonds between the Metal atom and the linker is broken and no.of bonds is less than the original bonds. Can this be due to the topology file created or am I missing something in mdp file. If anyone has experience with modeling MOFs using GROMACS, I really appreciate your help. Thank You ; minim.mdp - used as input into grompp to generate em.tpr integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 75.0 ; Stop minimization when the maximum force < 100.0 kJ/mol/nm emstep = 0.1 ; Energy step size nsteps = 1000 ; Maximum number of (minimization) steps to perform ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 1 ; Frequency to update the neighbor list and long range forces cutoff-scheme = Verlet ns_type = grid ; Method to determine neighbor list (simple, grid) coulombtype = Cut-off ; Treatment of long range electrostatic interactions rcoulomb = 2.0 ; Short-range electrostatic cut-off rvdw = 2.0 ; Short-range Van der Waals cut-off rlist = 2.0 ; Short-range neighbor cut-off pbc = xyz ; Periodic Boundary Conditions (yes/no) With Regards Nagasree Garapati Research Assistant Professor Dept of Chemical and Biomedical Engineering West Virginia University PO Box 6102 Morgantown, WV 26506-6102 304 293-5028<tel:304%20293-5028>(O) 304 276-3674(M) -- 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] .XYZ file format to .gro format
Hi I have structure of a molecule in .xyz format, is there an option similar to pdb2gmx in gromacs to convert .xyz file to .gro files? -- 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.
