Re: [gmx-users] Graphene topology file
Hi gromacs users, I was able to simulate graphene sheet in water. Now I want to simulate functionalised graphene sheet with -OH groups attached randomly to graphene sheet. I modified atomname2type.n2t file by adding oxygen and hydrogen groups to it. Following is my .n2t file: Copls_9950 12.011 2C 0.142 C 0.142 Copls_9960 12.011 3C 0.142 C 0.142 C 0.142 Copls_9970 12.011 1C 0.142 Copls_9980 12.011 4C 0.142 C 0.142 C 0.142 O 0.143 OH opls_154 -0.715.9994 2C 0.143 HO 0.96 HO opls_155 0.435 1.008 1OH 0.96 But when I give following x2top command, I get error message : g_x2top -f grap1.pdb -o graphene.top -name GRA -nexcl 3 -pbc Error: Fatal error: Could only find a forcefield type for 256 out of 456 atoms Can anyone please let me know what can be creating the problem? Thanks and Regards Sukriti Gupta Sukriti Gupta (Ms) | PhD Student | Energy Research Institute @ NTU (ERI@N) | Nanyang Technological University N1.3-B4-14, 50 Nanyang Avenue, Singapore 639798 Tel: (65) 81164191 GMT+8h | Email:sukriti...@e.ntu.edu.sg | Web:erian.ntu.edu.sg From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Justin Lemkul jalem...@vt.edu Sent: Thursday, July 17, 2014 7:50 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Graphene topology file On 7/17/14, 7:16 AM, #SUKRITI GUPTA# wrote: Hi gromacs users, I read that for slab geometries where you need pbc in xy, you can use pbc=xyz and have a slab of vacuum in between the periodic images in z and use ewald3dc (Yeh and Berkowitz method). So I changed my mdp file extended my box in z direction( with no solvent molecules) and did the energy minimization and npt again. In em, the box looks fine but with npt again I get same output i.e. water molecules fly away and box size in z direction increases drastically, through the vacuum layer is still maintained. Then I changed my pressure coupling to Parinello- Rahman instead of Berendsen. This time npt runs some steps and gives an error message: Fatal error: One of the box vectors has become shorter than twice the cut-off length or box_yy-|box_zy| or box_zz has become smaller than the cut-off. Can anyone please let me know how can I solve this problem. If we have a layer of vacuum, wont the box size reduce in npt and cause this error? Should I skip npt and directly do nvt? If you need to maintain a vacuum layer, your box needs to be incompressible along that direction, i.e. use semiisotropic coupling and set compressibility = 0 in the .mdp file for the z-direction. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- 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] Graphene topology file
On Mon, Aug 4, 2014 at 8:38 AM, #SUKRITI GUPTA# sukriti...@e.ntu.edu.sg wrote: Hi gromacs users, I was able to simulate graphene sheet in water. Now I want to simulate functionalised graphene sheet with -OH groups attached randomly to graphene sheet. I modified atomname2type.n2t file by adding oxygen and hydrogen groups to it. Following is my .n2t file: Copls_9950 12.011 2C 0.142 C 0.142 Copls_9960 12.011 3C 0.142 C 0.142 C 0.142 Copls_9970 12.011 1C 0.142 Copls_9980 12.011 4C 0.142 C 0.142 C 0.142 O 0.143 OH opls_154 -0.715.9994 2C 0.143 HO 0.96 HO opls_155 0.435 1.008 1OH 0.96 But when I give following x2top command, I get error message : g_x2top -f grap1.pdb -o graphene.top -name GRA -nexcl 3 -pbc Error: Fatal error: Could only find a forcefield type for 256 out of 456 atoms Can anyone please let me know what can be creating the problem? g_x2top will print to the screen all of the atoms that it had problems with. The error means that either your distance criteria are wrong or the geometry of the system is otherwise incompatible with the specifications in the .n2t file. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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] Graphene topology file
Hi gromacs users, I read that for slab geometries where you need pbc in xy, you can use pbc=xyz and have a slab of vacuum in between the periodic images in z and use ewald3dc (Yeh and Berkowitz method). So I changed my mdp file extended my box in z direction( with no solvent molecules) and did the energy minimization and npt again. In em, the box looks fine but with npt again I get same output i.e. water molecules fly away and box size in z direction increases drastically, through the vacuum layer is still maintained. Then I changed my pressure coupling to Parinello- Rahman instead of Berendsen. This time npt runs some steps and gives an error message: Fatal error: One of the box vectors has become shorter than twice the cut-off length or box_yy-|box_zy| or box_zz has become smaller than the cut-off. Can anyone please let me know how can I solve this problem. If we have a layer of vacuum, wont the box size reduce in npt and cause this error? Should I skip npt and directly do nvt? Regards Sukriti Sukriti Gupta (Ms) | PhD Student | Energy Research Institute @ NTU (ERI@N) | Nanyang Technological University N1.3-B4-14, 50 Nanyang Avenue, Singapore 639798 Tel: (65) 81164191 GMT+8h | Email:sukriti...@e.ntu.edu.sg | Web:erian.ntu.edu.sg From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of #SUKRITI GUPTA# sukriti...@e.ntu.edu.sg Sent: Wednesday, July 16, 2014 11:20 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Graphene topology file Dear Justin, Thanks so much for your help. I am still unable to solve the problem of blowing up of the box. Once I am able to do correct simulation I will update here. Regards Sukriti Sukriti Gupta (Ms) | PhD Student | Energy Research Institute @ NTU (ERI@N) | Nanyang Technological University N1.3-B4-14, 50 Nanyang Avenue, Singapore 639798 Tel: (65) 81164191 GMT+8h | Email:sukriti...@e.ntu.edu.sg | Web:erian.ntu.edu.sg From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Justin Lemkul jalem...@vt.edu Sent: Saturday, July 12, 2014 5:17 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Graphene topology file On 7/11/14, 5:42 AM, #SUKRITI GUPTA# wrote: Hi Justin, Thanks for the reply. I changed define= -dflexible to -dposres_water and removed freeze graphene group in my .mdp file and ran the energy minimization and npt again. This time for pbc= xyz, the water doesn't fly away but the graphene sheet curves and does not remain in xy plane. Is it ok for the sheet to bend during simulation and will it not effect the pbc? Applying pressure along the plane of the sheet can cause deformation. Whether or not this is physically relevant, I have no idea. Also for pbc=xy, the same problem persists as the previous one i.e. following error occurs: Step 20: The charge group starting at atom 796 moved than the distance allowed by the domain decomposition in direction X distance out of cell -0.290927 New coordinates:2.4112.0060.982 Old cell boundaries in direction X:0.0002.702 New cell boundaries in direction X:0.0002.702 --- Program mdrun, VERSION 4.5.5 Source code file: /build/buildd/gromacs-4.5.5/src/mdlib/domdec.c, line: 4124 Fatal error: A charge group moved too far between two domain decomposition steps This usually means that your system is not well equilibrated For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors. Can you please suggest what can be causing the error to occur? That's a generic error suggesting the system is blowing up. http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System I know nothing about using walls, so that's the best I can suggest. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- 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
Re: [gmx-users] Graphene topology file
On 7/17/14, 7:16 AM, #SUKRITI GUPTA# wrote: Hi gromacs users, I read that for slab geometries where you need pbc in xy, you can use pbc=xyz and have a slab of vacuum in between the periodic images in z and use ewald3dc (Yeh and Berkowitz method). So I changed my mdp file extended my box in z direction( with no solvent molecules) and did the energy minimization and npt again. In em, the box looks fine but with npt again I get same output i.e. water molecules fly away and box size in z direction increases drastically, through the vacuum layer is still maintained. Then I changed my pressure coupling to Parinello- Rahman instead of Berendsen. This time npt runs some steps and gives an error message: Fatal error: One of the box vectors has become shorter than twice the cut-off length or box_yy-|box_zy| or box_zz has become smaller than the cut-off. Can anyone please let me know how can I solve this problem. If we have a layer of vacuum, wont the box size reduce in npt and cause this error? Should I skip npt and directly do nvt? If you need to maintain a vacuum layer, your box needs to be incompressible along that direction, i.e. use semiisotropic coupling and set compressibility = 0 in the .mdp file for the z-direction. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Graphene topology file
Dear Justin, Thanks so much for your help. I am still unable to solve the problem of blowing up of the box. Once I am able to do correct simulation I will update here. Regards Sukriti Sukriti Gupta (Ms) | PhD Student | Energy Research Institute @ NTU (ERI@N) | Nanyang Technological University N1.3-B4-14, 50 Nanyang Avenue, Singapore 639798 Tel: (65) 81164191 GMT+8h | Email:sukriti...@e.ntu.edu.sg | Web:erian.ntu.edu.sg From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Justin Lemkul jalem...@vt.edu Sent: Saturday, July 12, 2014 5:17 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Graphene topology file On 7/11/14, 5:42 AM, #SUKRITI GUPTA# wrote: Hi Justin, Thanks for the reply. I changed define= -dflexible to -dposres_water and removed freeze graphene group in my .mdp file and ran the energy minimization and npt again. This time for pbc= xyz, the water doesn't fly away but the graphene sheet curves and does not remain in xy plane. Is it ok for the sheet to bend during simulation and will it not effect the pbc? Applying pressure along the plane of the sheet can cause deformation. Whether or not this is physically relevant, I have no idea. Also for pbc=xy, the same problem persists as the previous one i.e. following error occurs: Step 20: The charge group starting at atom 796 moved than the distance allowed by the domain decomposition in direction X distance out of cell -0.290927 New coordinates:2.4112.0060.982 Old cell boundaries in direction X:0.0002.702 New cell boundaries in direction X:0.0002.702 --- Program mdrun, VERSION 4.5.5 Source code file: /build/buildd/gromacs-4.5.5/src/mdlib/domdec.c, line: 4124 Fatal error: A charge group moved too far between two domain decomposition steps This usually means that your system is not well equilibrated For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors. Can you please suggest what can be causing the error to occur? That's a generic error suggesting the system is blowing up. http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System I know nothing about using walls, so that's the best I can suggest. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- 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] Graphene topology file
Hi Justin, Thanks for the reply. I changed define= -dflexible to -dposres_water and removed freeze graphene group in my .mdp file and ran the energy minimization and npt again. This time for pbc= xyz, the water doesn't fly away but the graphene sheet curves and does not remain in xy plane. Is it ok for the sheet to bend during simulation and will it not effect the pbc? Also for pbc=xy, the same problem persists as the previous one i.e. following error occurs: Step 20: The charge group starting at atom 796 moved than the distance allowed by the domain decomposition in direction X distance out of cell -0.290927 New coordinates:2.4112.0060.982 Old cell boundaries in direction X:0.0002.702 New cell boundaries in direction X:0.0002.702 --- Program mdrun, VERSION 4.5.5 Source code file: /build/buildd/gromacs-4.5.5/src/mdlib/domdec.c, line: 4124 Fatal error: A charge group moved too far between two domain decomposition steps This usually means that your system is not well equilibrated For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors. Can you please suggest what can be causing the error to occur? Thanks and Regards Sukriti From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Justin Lemkul jalem...@vt.edu Sent: Thursday, July 10, 2014 8:50 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Graphene topology file On 7/10/14, 8:46 AM, #SUKRITI GUPTA# wrote: Hi Justin, Thanks for the reply. Following is my npt.mdp file for pbc in xy direction: title = example cpp = define = -DFLEXIBLE You shouldn't use flexible water during MD. The water models in Gromacs were designed to be rigid. constraints = none integrator = md dt = 0.001 nsteps = 10 ;Output control parameters nstxout = 100 nstvout = 100 nstfout = 0 ;Checking for crashes nstcheckpoint = 1000 ; Output frequency for energies to log file and energy file nstlog = 100 nstenergy = 100 ; Output frequency and precision for xtc file nstxtcout = 0 xtc-precision = 1000 ; NEIGHBORSEARCHING PARAMETERS ; nblist update frequency nstlist = 10 ; ns algorithm (simple or grid) ns-type = Grid ; Periodic boundary conditions: xyz (default), no (vacuum) ; or full (infinite systems only) pbc = xy ; nblist cut-off domain-decomposition= no rlist = 1.2 ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = Cut-off rcoulomb-switch = 0 rcoulomb= 1.2 ; ; Method for doing Van der Waals vdw-type= Switch ; cut-off lengths rvdw-switch = 0 rvdw= 1.0 ; OPTIONS FOR WEAK COUPLING ALGORITHMS ; Temperature coupling = yes tcoupl = Berendsen The Berendsen algorithm has known deficiencies. For initial equilibration, it's OK, but don't use it for a production simulation. ; Groups to couple separately tc-grps = Other SOL ; Time constant (ps) and reference temperature (K) tau-t= .25 .25 ref-t= 300 300 ; Pressure coupling Pcoupl = Berendsen Pcoupltype = Semiisotropic ; Time constant (ps), compressibility (1/bar) and reference P (bar) tau-p = 1 1 compressibility = 0 4.5e-5 ref-p= 1.01325 1.01325 ; ; GENERATE VELOCITIES FOR STARTUP RUN gen-vel = yes gen-temp = 300 gen-seed= 173529 nwall = 2 wall_type = 12-6 wall_density = 5 5 wall_atomtype = opls_995 opls_996 wall_r_linpot = 1 wall_ewald_zfac = 3 periodic_molecules=yes freezegrps = GRA freezedim = Y Y Y Freezing the graphene is probably going to generate a lot of problems. You get totally unphysical forces unless you use energygrp_excl properly, but even then, freezing is a severe perturbation to the system. For pbc in xyz, nwall options are not there and I used Isotropic Pcoupletype with compressibility 4.5e-5. Gromacs Userlist is not allowing me to attach images as the size of the mail is increasing to more than 50KB. So can I mail the images to your mail id? No. Post them to an image-sharing site and provide a URL. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441
Re: [gmx-users] Graphene topology file
On 7/11/14, 5:42 AM, #SUKRITI GUPTA# wrote: Hi Justin, Thanks for the reply. I changed define= -dflexible to -dposres_water and removed freeze graphene group in my .mdp file and ran the energy minimization and npt again. This time for pbc= xyz, the water doesn't fly away but the graphene sheet curves and does not remain in xy plane. Is it ok for the sheet to bend during simulation and will it not effect the pbc? Applying pressure along the plane of the sheet can cause deformation. Whether or not this is physically relevant, I have no idea. Also for pbc=xy, the same problem persists as the previous one i.e. following error occurs: Step 20: The charge group starting at atom 796 moved than the distance allowed by the domain decomposition in direction X distance out of cell -0.290927 New coordinates:2.4112.0060.982 Old cell boundaries in direction X:0.0002.702 New cell boundaries in direction X:0.0002.702 --- Program mdrun, VERSION 4.5.5 Source code file: /build/buildd/gromacs-4.5.5/src/mdlib/domdec.c, line: 4124 Fatal error: A charge group moved too far between two domain decomposition steps This usually means that your system is not well equilibrated For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors. Can you please suggest what can be causing the error to occur? That's a generic error suggesting the system is blowing up. http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System I know nothing about using walls, so that's the best I can suggest. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Graphene topology file
On 7/10/14, 1:29 AM, #SUKRITI GUPTA# wrote: Hi Justin, I did simulation 2 times, once with PBC in xy with walls and other time with pbc in xyz. For pbc in xy with walls with following wall parameters: nwall = 2 wall_type = 12-6 wall_density = 5 5 wall_atomtype = opls_995 opls_996 wall_r_linpot = 1 wall_ewald_zfac = 3 Energy minimization runs fine but npt shows following errror and is terminated: Step 20: The charge group starting at atom 796 moved than the distance allowed by the domain decomposition in direction X distance out of cell -0.290927 New coordinates:2.4112.0060.982 Old cell boundaries in direction X:0.0002.702 New cell boundaries in direction X:0.0002.702 --- Program mdrun, VERSION 4.5.5 Source code file: /build/buildd/gromacs-4.5.5/src/mdlib/domdec.c, line: 4124 Fatal error: A charge group moved too far between two domain decomposition steps This usually means that your system is not well equilibrated For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors For pbc in xyz, both energy minimization and npt run but the water is suddenly moving far away from the graphene sheet any tries to agglomerate together causing the box size to increase drastically. It is almost like the box is about to explode. Its size changes from (2.70200 2.55300 4.0) to (11.46117 10.82915 16.96695). The box expands in x,y and z all directions. Without full .mdp files and some images demonstrating what's going on, it's too hard to guess at what's happening here. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Graphene topology file
Hi Justin, Thanks for the reply. Following is my npt.mdp file for pbc in xy direction: title = example cpp = define = -DFLEXIBLE constraints = none integrator = md dt = 0.001 nsteps = 10 ;Output control parameters nstxout = 100 nstvout = 100 nstfout = 0 ;Checking for crashes nstcheckpoint = 1000 ; Output frequency for energies to log file and energy file nstlog = 100 nstenergy = 100 ; Output frequency and precision for xtc file nstxtcout = 0 xtc-precision = 1000 ; NEIGHBORSEARCHING PARAMETERS ; nblist update frequency nstlist = 10 ; ns algorithm (simple or grid) ns-type = Grid ; Periodic boundary conditions: xyz (default), no (vacuum) ; or full (infinite systems only) pbc = xy ; nblist cut-off domain-decomposition= no rlist = 1.2 ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = Cut-off rcoulomb-switch = 0 rcoulomb= 1.2 ; ; Method for doing Van der Waals vdw-type= Switch ; cut-off lengths rvdw-switch = 0 rvdw= 1.0 ; OPTIONS FOR WEAK COUPLING ALGORITHMS ; Temperature coupling = yes tcoupl = Berendsen ; Groups to couple separately tc-grps = Other SOL ; Time constant (ps) and reference temperature (K) tau-t= .25 .25 ref-t= 300 300 ; Pressure coupling Pcoupl = Berendsen Pcoupltype = Semiisotropic ; Time constant (ps), compressibility (1/bar) and reference P (bar) tau-p = 1 1 compressibility = 0 4.5e-5 ref-p= 1.01325 1.01325 ; ; GENERATE VELOCITIES FOR STARTUP RUN gen-vel = yes gen-temp = 300 gen-seed= 173529 nwall = 2 wall_type = 12-6 wall_density = 5 5 wall_atomtype = opls_995 opls_996 wall_r_linpot = 1 wall_ewald_zfac = 3 periodic_molecules=yes freezegrps = GRA freezedim = Y Y Y For pbc in xyz, nwall options are not there and I used Isotropic Pcoupletype with compressibility 4.5e-5. Gromacs Userlist is not allowing me to attach images as the size of the mail is increasing to more than 50KB. So can I mail the images to your mail id? Regards Sukriti Gupta Sukriti Gupta (Ms) | PhD Student | Energy Research Institute @ NTU (ERI@N) | Nanyang Technological University Interdisciplinary Graduate School | Office: N1.3-B4-14, 62 Nanyang Drive, Singapore(637459) Tel: (65) 81164191 GMT+8h | Email:sukriti...@e.ntu.edu.sg | Web:erian.ntu.edu.sg From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Justin Lemkul jalem...@vt.edu Sent: Thursday, July 10, 2014 8:28 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Graphene topology file On 7/10/14, 1:29 AM, #SUKRITI GUPTA# wrote: Hi Justin, I did simulation 2 times, once with PBC in xy with walls and other time with pbc in xyz. For pbc in xy with walls with following wall parameters: nwall = 2 wall_type = 12-6 wall_density = 5 5 wall_atomtype = opls_995 opls_996 wall_r_linpot = 1 wall_ewald_zfac = 3 Energy minimization runs fine but npt shows following errror and is terminated: Step 20: The charge group starting at atom 796 moved than the distance allowed by the domain decomposition in direction X distance out of cell -0.290927 New coordinates:2.4112.0060.982 Old cell boundaries in direction X:0.0002.702 New cell boundaries in direction X:0.0002.702 --- Program mdrun, VERSION 4.5.5 Source code file: /build/buildd/gromacs-4.5.5/src/mdlib/domdec.c, line: 4124 Fatal error: A charge group moved too far between two domain decomposition steps This usually means that your system is not well equilibrated For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors For pbc in xyz, both energy minimization and npt run but the water is suddenly moving far away from the graphene sheet any tries to agglomerate together causing the box size to increase drastically. It is almost like the box is about to explode. Its size changes from (2.70200 2.55300 4.0) to (11.46117 10.82915 16.96695). The box expands in x,y and z all directions. Without full .mdp files and some images demonstrating what's going on, it's too hard to guess at what's happening here. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601
Re: [gmx-users] Graphene topology file
On 7/10/14, 8:46 AM, #SUKRITI GUPTA# wrote: Hi Justin, Thanks for the reply. Following is my npt.mdp file for pbc in xy direction: title = example cpp = define = -DFLEXIBLE You shouldn't use flexible water during MD. The water models in Gromacs were designed to be rigid. constraints = none integrator = md dt = 0.001 nsteps = 10 ;Output control parameters nstxout = 100 nstvout = 100 nstfout = 0 ;Checking for crashes nstcheckpoint = 1000 ; Output frequency for energies to log file and energy file nstlog = 100 nstenergy = 100 ; Output frequency and precision for xtc file nstxtcout = 0 xtc-precision = 1000 ; NEIGHBORSEARCHING PARAMETERS ; nblist update frequency nstlist = 10 ; ns algorithm (simple or grid) ns-type = Grid ; Periodic boundary conditions: xyz (default), no (vacuum) ; or full (infinite systems only) pbc = xy ; nblist cut-off domain-decomposition= no rlist = 1.2 ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = Cut-off rcoulomb-switch = 0 rcoulomb= 1.2 ; ; Method for doing Van der Waals vdw-type= Switch ; cut-off lengths rvdw-switch = 0 rvdw= 1.0 ; OPTIONS FOR WEAK COUPLING ALGORITHMS ; Temperature coupling = yes tcoupl = Berendsen The Berendsen algorithm has known deficiencies. For initial equilibration, it's OK, but don't use it for a production simulation. ; Groups to couple separately tc-grps = Other SOL ; Time constant (ps) and reference temperature (K) tau-t= .25 .25 ref-t= 300 300 ; Pressure coupling Pcoupl = Berendsen Pcoupltype = Semiisotropic ; Time constant (ps), compressibility (1/bar) and reference P (bar) tau-p = 1 1 compressibility = 0 4.5e-5 ref-p= 1.01325 1.01325 ; ; GENERATE VELOCITIES FOR STARTUP RUN gen-vel = yes gen-temp = 300 gen-seed= 173529 nwall = 2 wall_type = 12-6 wall_density = 5 5 wall_atomtype = opls_995 opls_996 wall_r_linpot = 1 wall_ewald_zfac = 3 periodic_molecules=yes freezegrps = GRA freezedim = Y Y Y Freezing the graphene is probably going to generate a lot of problems. You get totally unphysical forces unless you use energygrp_excl properly, but even then, freezing is a severe perturbation to the system. For pbc in xyz, nwall options are not there and I used Isotropic Pcoupletype with compressibility 4.5e-5. Gromacs Userlist is not allowing me to attach images as the size of the mail is increasing to more than 50KB. So can I mail the images to your mail id? No. Post them to an image-sharing site and provide a URL. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Graphene topology file
On 7/9/14, 9:06 AM, #SUKRITI GUPTA# wrote: Thanks for the reply Justin. I just checked my box size again and found it to be smaller than the required. Hence I changed the size and ran the simulation again. This time energy minimization happened correctly without any change in the graphene structure. But when I am doing npt, the water is suddenly moving far away from the graphene sheet any tries to agglomerate together causing the box size to increase drastically. It is almost like the box is about to explode. Its size changes from 2.5A to 11A. Can you please help me figure out the problem. Does the box expand along z? Are you using walls? If not, you should be, in the case of pbc = xy. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Graphene topology file
Hi Justin, I did simulation 2 times, once with PBC in xy with walls and other time with pbc in xyz. For pbc in xy with walls with following wall parameters: nwall = 2 wall_type = 12-6 wall_density = 5 5 wall_atomtype = opls_995 opls_996 wall_r_linpot = 1 wall_ewald_zfac = 3 Energy minimization runs fine but npt shows following errror and is terminated: Step 20: The charge group starting at atom 796 moved than the distance allowed by the domain decomposition in direction X distance out of cell -0.290927 New coordinates:2.4112.0060.982 Old cell boundaries in direction X:0.0002.702 New cell boundaries in direction X:0.0002.702 --- Program mdrun, VERSION 4.5.5 Source code file: /build/buildd/gromacs-4.5.5/src/mdlib/domdec.c, line: 4124 Fatal error: A charge group moved too far between two domain decomposition steps This usually means that your system is not well equilibrated For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors For pbc in xyz, both energy minimization and npt run but the water is suddenly moving far away from the graphene sheet any tries to agglomerate together causing the box size to increase drastically. It is almost like the box is about to explode. Its size changes from (2.70200 2.55300 4.0) to (11.46117 10.82915 16.96695). The box expands in x,y and z all directions. Thanks and Regards Sukriti Sukriti Gupta (Ms) | PhD Student | Energy Research Institute @ NTU (ERI@N) | Nanyang Technological University Interdisciplinary Graduate School | Office: N1.3-B4-14, 62 Nanyang Drive, Singapore(637459) Tel: (65) 81164191 GMT+8h | Email:sukriti...@e.ntu.edu.sg | Web:erian.ntu.edu.sg From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Justin Lemkul jalem...@vt.edu Sent: Thursday, July 10, 2014 1:26 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Graphene topology file On 7/9/14, 9:06 AM, #SUKRITI GUPTA# wrote: Thanks for the reply Justin. I just checked my box size again and found it to be smaller than the required. Hence I changed the size and ran the simulation again. This time energy minimization happened correctly without any change in the graphene structure. But when I am doing npt, the water is suddenly moving far away from the graphene sheet any tries to agglomerate together causing the box size to increase drastically. It is almost like the box is about to explode. Its size changes from 2.5A to 11A. Can you please help me figure out the problem. Does the box expand along z? Are you using walls? If not, you should be, in the case of pbc = xy. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- 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] Graphene topology file
On 7/8/14, 1:23 AM, #SUKRITI GUPTA# wrote: Hi Justin, Thanks a lot for your replies. I want to simulate a half cell with graphene electrode only on one side, hence i am using pbc in only xy direction i.e. direction of graphene sheet, so that I have a infinite size graphene sheet with no side effects. But if I use 3D pbc then graphene sheet effect will be there on the other side of the box also, which I don't want. Also if I use 3D PBC or 2D PBC, the major problem is that even after freezing graphene sheet, after doing energy minimization, the sheet remains linear but becomes distorted and new bonds are formed between terminal carbons. I don't know what is the problem with my system. That sounds like a topology problem. Using periodic_molecules = yes should allow for bonding across periodic boundaries, so bonds shouldn't be recognized between atoms at the ends of your sheet within the unit cell. Is that what you're describing? Images would help. Check the topology carefully to make sure it has been constructed properly. A correctly sized box with g_x2top -pbc should create a sensible topology. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Graphene topology file
Hi Abhijit, Following is my mdp file: ; VARIOUS PREPROCESSING OPTIONS title= cpp= /lib/cpp include = define = -DFLEXIBLE ; RUN CONTROL PARAMETERS integrator = l_bfgs ; Start time and timestep in ps tinit= 0 dt = 0.001 nsteps = 5000 ; For exact run continuation or redoing part of a run init_step= 0 ; mode for center of mass motion removal comm-mode= Linear ; number of steps for center of mass motion removal nstcomm = 1 ; ENERGY MINIMIZATION OPTIONS ; Force tolerance and initial step-size emtol= 10 emstep = 0.01 ; Max number of iterations in relax_shells niter= 20 ; Step size (1/ps^2) for minimization of flexible constraints fcstep = 0 ; Frequency of steepest descents steps when doing CG nstcgsteep = 1000 nbfgscorr= 10 ; OUTPUT CONTROL OPTIONS ; Output frequency for coords (x), velocities (v) and forces (f) nstxout = 100 nstvout = 100 nstfout = 100 ; Checkpointing helps you continue after crashes nstcheckpoint= 1000 ; Output frequency for energies to log file and energy file nstlog = 100 nstenergy= 100 ; Output frequency and precision for xtc file nstxtcout= 0 xtc-precision= 1000 ; This selects the subset of atoms for the xtc file. You can ; NEIGHBORSEARCHING PARAMETERS ; nblist update frequency nstlist = 10 ; ns algorithm (simple or grid) ns-type = Grid ; Periodic boundary conditions: xyz (default), no (vacuum) ; or full (infinite systems only) pbc = xy ; nblist cut-off rlist= 1.2 domain-decomposition = no ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = Cut-off rcoulomb = 1.2 ; Method for doing Van der Waals vdw-type = Switch ; cut-off lengths rvdw-switch = 0 rvdw = 1.0 ; Apply long range dispersi0n corrections for Energy and Pressure DispCorr = No ; Extension of the potential lookup tables beyond the cut-off table-extension = 2 ; Spacing for the PME/PPPM FFT grid fourierspacing = 0.12 ; FFT grid size, when a value is 0 fourierspacing will be used fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 ; EWALD/PME/PPPM parameters pme_order= 4 ewald_rtol = 4e-05 ewald_geometry = 3d epsilon_surface = 0 optimize_fft = no ; GENERATE VELOCITIES FOR STARTUP RUN gen-vel = no gen-temp = 300 gen-seed = 173529 periodic_molecules=yes freezegrps = GRA freezedim = Y Y Y Sukriti Gupta (Ms) | PhD Student | Energy Research Institute @ NTU (ERI@N) | Nanyang Technological University Interdisciplinary Graduate School | Office: N1.3-B4-14, 62 Nanyang Drive, Singapore(637459) Tel: (65) 81164191 GMT+8h | Email:sukriti...@e.ntu.edu.sg | Web:erian.ntu.edu.sg From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of abhijit Kayal abhijitchemi...@gmail.com Sent: Monday, July 7, 2014 1:21 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Graphene topology file Hi Sukriti, Can you post your .mdp file of energy minimization? The problem is not because there are no terminal H atoms. If you want periodic boundary conditions only x-y direction then you have to use nwall in .mdp file. Thanks Abhijit On Mon, Jul 7, 2014 at 10:06 AM, #SUKRITI GUPTA# sukriti...@e.ntu.edu.sg wrote: Hi all, After getting the topology file for graphene, when i tried to freeze graphene and do energy minimization with just water molecules around it, then the graphene structure becomes distorted ie. the upper layer of the graphene shifts down and the terminal carbons forms bond with each other. I think this happens because i did not add terminal hydrogens to the graphene sheet as I wanted periodic boundary conditions in x y direction. Also the box size in z direction is shown to be zero in the output file of energy minimization. Can anyone please let me know how to solve this problem? Thanks, Sukriti Sukriti Gupta (Ms) | PhD Student | Energy Research Institute @ NTU (ERI@N) | Nanyang Technological University Interdisciplinary Graduate School | Office: N1.3-B4-14, 62 Nanyang Drive, Singapore(637459) Tel: (65) 81164191 GMT+8h | Email:sukriti...@e.ntu.edu.sg | Web: erian.ntu.edu.sg From: gromacs.org_gmx-users-boun
Re: [gmx-users] Graphene topology file
On 7/7/14, 12:36 AM, #SUKRITI GUPTA# wrote: Hi all, After getting the topology file for graphene, when i tried to freeze graphene and do energy minimization with just water molecules around it, then the graphene structure becomes distorted ie. the upper layer of the graphene shifts down and the terminal carbons forms bond with each other. I think this happens because i did not add terminal hydrogens to the graphene sheet as I wanted periodic boundary conditions in x y direction. Also the box size in z direction is shown to be zero in the output file of energy minimization. Can anyone please let me know how to solve this problem? If the z-dimension is zero, then your box isn't set up properly. Likely you're just getting clashes between periodic images. Setting up a proper box should solve the problem. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Graphene topology file
Hi Justin, Thanks for the reply. Actually I am having the problem of z- dimension to be zero only when I am giving pbc only in xy direction. For pbc in xyz, the z dimension is not becoming zero. So do you still think it can be because of improper box size chosen? Also I have not given nwall option in .mdp file. As Abhijit suggested, it can create a problem. I do not have any idea about nwall functioning and what parameters to choose for it to work with xy periodic graphene sheet. I am unable to find any tutorial about this also. Can you please suggest me what to do for this. Thanks and Regards Sukriti Sukriti Gupta (Ms) | PhD Student | Energy Research Institute @ NTU (ERI@N) | Nanyang Technological University Interdisciplinary Graduate School | Office: N1.3-B4-14, 62 Nanyang Drive, Singapore(637459) Tel: (65) 81164191 GMT+8h | Email:sukriti...@e.ntu.edu.sg | Web:erian.ntu.edu.sg From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Justin Lemkul jalem...@vt.edu Sent: Monday, July 7, 2014 6:09 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Graphene topology file On 7/7/14, 12:36 AM, #SUKRITI GUPTA# wrote: Hi all, After getting the topology file for graphene, when i tried to freeze graphene and do energy minimization with just water molecules around it, then the graphene structure becomes distorted ie. the upper layer of the graphene shifts down and the terminal carbons forms bond with each other. I think this happens because i did not add terminal hydrogens to the graphene sheet as I wanted periodic boundary conditions in x y direction. Also the box size in z direction is shown to be zero in the output file of energy minimization. Can anyone please let me know how to solve this problem? If the z-dimension is zero, then your box isn't set up properly. Likely you're just getting clashes between periodic images. Setting up a proper box should solve the problem. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- 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] Graphene topology file
On 7/7/14, 7:54 AM, #SUKRITI GUPTA# wrote: Hi Justin, Thanks for the reply. Actually I am having the problem of z- dimension to be zero only when I am giving pbc only in xy direction. For pbc in xyz, the z dimension is not becoming zero. So do you still think it can be because of improper box size chosen? No, the z-dimension would not be relevant with pbc = xy. Also I have not given nwall option in .mdp file. As Abhijit suggested, it can create a problem. I do not have any idea about nwall functioning and what parameters to choose for it to work with xy periodic graphene sheet. I am unable to find any tutorial about this also. Can you please suggest me what to do for this. The manual discusses walls in great detail, though they're not required in this case. What reason do you have for only using 2-D PBC? Why not 3-D (pbc = xyz)? -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Graphene topology file
Hi Justin, Thanks a lot for your replies. I want to simulate a half cell with graphene electrode only on one side, hence i am using pbc in only xy direction i.e. direction of graphene sheet, so that I have a infinite size graphene sheet with no side effects. But if I use 3D pbc then graphene sheet effect will be there on the other side of the box also, which I don't want. Also if I use 3D PBC or 2D PBC, the major problem is that even after freezing graphene sheet, after doing energy minimization, the sheet remains linear but becomes distorted and new bonds are formed between terminal carbons. I don't know what is the problem with my system. Regards Sukriti Sukriti Gupta (Ms) | PhD Student | Energy Research Institute @ NTU (ERI@N) | Nanyang Technological University Interdisciplinary Graduate School | Office: N1.3-B4-14, 62 Nanyang Drive, Singapore(637459) Tel: (65) 81164191 GMT+8h | Email:sukriti...@e.ntu.edu.sg | Web:erian.ntu.edu.sg From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Justin Lemkul jalem...@vt.edu Sent: Tuesday, July 8, 2014 12:44 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Graphene topology file On 7/7/14, 7:54 AM, #SUKRITI GUPTA# wrote: Hi Justin, Thanks for the reply. Actually I am having the problem of z- dimension to be zero only when I am giving pbc only in xy direction. For pbc in xyz, the z dimension is not becoming zero. So do you still think it can be because of improper box size chosen? No, the z-dimension would not be relevant with pbc = xy. Also I have not given nwall option in .mdp file. As Abhijit suggested, it can create a problem. I do not have any idea about nwall functioning and what parameters to choose for it to work with xy periodic graphene sheet. I am unable to find any tutorial about this also. Can you please suggest me what to do for this. The manual discusses walls in great detail, though they're not required in this case. What reason do you have for only using 2-D PBC? Why not 3-D (pbc = xyz)? -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- 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] Graphene topology file
Hi Sukirti, Try the following and additionally if you want force and angle constant you can also mention in g_x2top. g_x2top -f gra.pdb -o gra.top -name GRA -nexcl 3 -pbc You have to mention periodic_molecules=yes in the .mdp file. Thanks Abhijit On Fri, Jul 4, 2014 at 1:04 PM, #SUKRITI GUPTA# sukriti...@e.ntu.edu.sg wrote: Hi Abhijit, My g_x2top command is: g_x2top -f gra_2.pdb -o graphene.top -ff oplsaa -name graphene -noparam -pbc The grompp output is: ERROR 4100 [file graphene.top, line 10448]: ; (for all the lines, I have copied here only one line.) No default Ryckaert-Bell. types Excluding 3 bonded neighbours molecule type 'graphene' --- Program grompp, VERSION 4.5.5 Source code file: /build/buildd/gromacs-4.5.5/src/kernel/toppush.c, line: 1987 Fatal error: No such moleculetype SOL For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Thanks Sukriti Sukriti Gupta (Ms) | PhD Student | Energy Research Institute @ NTU (ERI@N) | Nanyang Technological University Interdisciplinary Graduate School | Office: N1.3-B4-14, 62 Nanyang Drive, Singapore(637459) Tel: (65) 81164191 GMT+8h | Email:sukriti...@e.ntu.edu.sg | Web: erian.ntu.edu.sg From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of abhijit Kayal abhijitchemi...@gmail.com Sent: Friday, July 4, 2014 2:21 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Graphene topology file Hi Sukriti, Can you tell me the g_x2top command you have given and the grompp output. Thanks Abhijit On Fri, Jul 4, 2014 at 10:01 AM, #SUKRITI GUPTA# sukriti...@e.ntu.edu.sg wrote: Dear Justin and Abhijit, Thanks a lot for your help. Now I am able to make the topology file but while doing grompp for energy minimisation its not taking the dihedral values on its own. Regards Sukriti Sukriti Gupta (Ms) | PhD Student | Energy Research Institute @ NTU (ERI@N ) | Nanyang Technological University Interdisciplinary Graduate School | Office: N1.3-B4-14, 62 Nanyang Drive, Singapore(637459) Tel: (65) 81164191 GMT+8h | Email:sukriti...@e.ntu.edu.sg | Web: erian.ntu.edu.sg From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of abhijit Kayal abhijitchemi...@gmail.com Sent: Thursday, July 3, 2014 6:43 PM To: gmx-us...@gromacs.org; vvcha...@gmail.com Subject: Re: [gmx-users] Graphene topology file Hi Sukriti, Copy the oplsaa.ff directory to your working directory. Then in ffnonbonded.itp file add the following lines.. opls_995 C 612.01100 0.000 A3.4e-01 3.61200e-01 opls_996 C 612.01100 0.000 A3.4e-01 3.61200e-01 opls_997 C 612.01100 0.000 A3.4e-01 3.61200e-01 Then in atomname2type.n2t file add the following lines. Copls_9950 12.011 2C 0.142 C 0.142 Copls_9960 12.011 3C 0.142 C 0.142 C 0.142 Copls_9970 12.011 1C 0.142 Then use g_x2top. This will work. Thanks Abhijit On Thu, Jul 3, 2014 at 3:11 PM, Dr. Vitaly Chaban vvcha...@gmail.com wrote: Graphene topology is like for tube, so C C C ... C ... C C C C C to the N2T file and you are done. Dr. Vitaly V. Chaban On Wed, Jul 2, 2014 at 5:29 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/2/14, 9:56 AM, #SUKRITI GUPTA# wrote: Dear all, I want to simulate graphite in water, for which i am trying to create a topology file for graphite. As its .rtp file cannot be written correctly, i tried to use g_x2top command following the steps given in following tutorial. http://chembytes.wikidot.com/grocnt But I think this tutorial is quite old and hence suitable for older version of gromacs as it still uses FF.dat file. Moreover if i am trying to make a new forcefield directory with name graphite_oplsaa containing the modified files like .n2t,.rtp and .itp, its giving me an error that Could not find force field 'graphite_oplsaa' in current directory, install tree or GMXDATA path. When I try to add this forcefield in original path ie. user/share/gromacs/top, it does not allow me to do that as i am not the administrator. Can anyone please let me know how to create the topology file. I require 3 graphene sheets with pbc. I have created the .pdb file using nanobuilder in vmd. The tutorial is indeed outdated but the logic is fairly sound. You don't
Re: [gmx-users] Graphene topology file
Hi Abhijit, Thanks for the reply. Now it is working. Regards Sukriti Sukriti Gupta (Ms) | PhD Student | Energy Research Institute @ NTU (ERI@N) | Nanyang Technological University Interdisciplinary Graduate School | Office: N1.3-B4-14, 62 Nanyang Drive, Singapore(637459) Tel: (65) 81164191 GMT+8h | Email:sukriti...@e.ntu.edu.sg | Web:erian.ntu.edu.sg From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of abhijit Kayal abhijitchemi...@gmail.com Sent: Friday, July 4, 2014 4:14 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Graphene topology file Hi Sukirti, Try the following and additionally if you want force and angle constant you can also mention in g_x2top. g_x2top -f gra.pdb -o gra.top -name GRA -nexcl 3 -pbc You have to mention periodic_molecules=yes in the .mdp file. Thanks Abhijit On Fri, Jul 4, 2014 at 1:04 PM, #SUKRITI GUPTA# sukriti...@e.ntu.edu.sg wrote: Hi Abhijit, My g_x2top command is: g_x2top -f gra_2.pdb -o graphene.top -ff oplsaa -name graphene -noparam -pbc The grompp output is: ERROR 4100 [file graphene.top, line 10448]: ; (for all the lines, I have copied here only one line.) No default Ryckaert-Bell. types Excluding 3 bonded neighbours molecule type 'graphene' --- Program grompp, VERSION 4.5.5 Source code file: /build/buildd/gromacs-4.5.5/src/kernel/toppush.c, line: 1987 Fatal error: No such moleculetype SOL For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Thanks Sukriti Sukriti Gupta (Ms) | PhD Student | Energy Research Institute @ NTU (ERI@N) | Nanyang Technological University Interdisciplinary Graduate School | Office: N1.3-B4-14, 62 Nanyang Drive, Singapore(637459) Tel: (65) 81164191 GMT+8h | Email:sukriti...@e.ntu.edu.sg | Web: erian.ntu.edu.sg From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of abhijit Kayal abhijitchemi...@gmail.com Sent: Friday, July 4, 2014 2:21 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Graphene topology file Hi Sukriti, Can you tell me the g_x2top command you have given and the grompp output. Thanks Abhijit On Fri, Jul 4, 2014 at 10:01 AM, #SUKRITI GUPTA# sukriti...@e.ntu.edu.sg wrote: Dear Justin and Abhijit, Thanks a lot for your help. Now I am able to make the topology file but while doing grompp for energy minimisation its not taking the dihedral values on its own. Regards Sukriti Sukriti Gupta (Ms) | PhD Student | Energy Research Institute @ NTU (ERI@N ) | Nanyang Technological University Interdisciplinary Graduate School | Office: N1.3-B4-14, 62 Nanyang Drive, Singapore(637459) Tel: (65) 81164191 GMT+8h | Email:sukriti...@e.ntu.edu.sg | Web: erian.ntu.edu.sg From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of abhijit Kayal abhijitchemi...@gmail.com Sent: Thursday, July 3, 2014 6:43 PM To: gmx-us...@gromacs.org; vvcha...@gmail.com Subject: Re: [gmx-users] Graphene topology file Hi Sukriti, Copy the oplsaa.ff directory to your working directory. Then in ffnonbonded.itp file add the following lines.. opls_995 C 612.01100 0.000 A3.4e-01 3.61200e-01 opls_996 C 612.01100 0.000 A3.4e-01 3.61200e-01 opls_997 C 612.01100 0.000 A3.4e-01 3.61200e-01 Then in atomname2type.n2t file add the following lines. Copls_9950 12.011 2C 0.142 C 0.142 Copls_9960 12.011 3C 0.142 C 0.142 C 0.142 Copls_9970 12.011 1C 0.142 Then use g_x2top. This will work. Thanks Abhijit On Thu, Jul 3, 2014 at 3:11 PM, Dr. Vitaly Chaban vvcha...@gmail.com wrote: Graphene topology is like for tube, so C C C ... C ... C C C C C to the N2T file and you are done. Dr. Vitaly V. Chaban On Wed, Jul 2, 2014 at 5:29 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/2/14, 9:56 AM, #SUKRITI GUPTA# wrote: Dear all, I want to simulate graphite in water, for which i am trying to create a topology file for graphite. As its .rtp file cannot be written correctly, i tried to use g_x2top command following the steps given in following tutorial. http://chembytes.wikidot.com/grocnt But I think this tutorial is quite old and hence suitable for older version of gromacs as it still uses FF.dat file
Re: [gmx-users] Graphene topology file
Graphene topology is like for tube, so C C C ... C ... C C C C C to the N2T file and you are done. Dr. Vitaly V. Chaban On Wed, Jul 2, 2014 at 5:29 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/2/14, 9:56 AM, #SUKRITI GUPTA# wrote: Dear all, I want to simulate graphite in water, for which i am trying to create a topology file for graphite. As its .rtp file cannot be written correctly, i tried to use g_x2top command following the steps given in following tutorial. http://chembytes.wikidot.com/grocnt But I think this tutorial is quite old and hence suitable for older version of gromacs as it still uses FF.dat file. Moreover if i am trying to make a new forcefield directory with name graphite_oplsaa containing the modified files like .n2t,.rtp and .itp, its giving me an error that Could not find force field 'graphite_oplsaa' in current directory, install tree or GMXDATA path. When I try to add this forcefield in original path ie. user/share/gromacs/top, it does not allow me to do that as i am not the administrator. Can anyone please let me know how to create the topology file. I require 3 graphene sheets with pbc. I have created the .pdb file using nanobuilder in vmd. The tutorial is indeed outdated but the logic is fairly sound. You don't have to modify anything in $GMXLIB (system-wide); you can just create an .n2t file in the working directory and it will override the one at the force field level. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- 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] Graphene topology file
On 7/3/14, 12:48 AM, #SUKRITI GUPTA# wrote: Dear Justin, Thanks for the reply but I am writing the .n2t file still getting the error that Could not find force field 'graphite_oplsaa' in current directory, install tree or GMXDATA path. What should I do? Moreover i don't think that n2t file tells program to use graphite_oplsaa force field. Well, as noted before, the tutorial there relies on a very old setup, so you shouldn't be following it exactly. The better approach is to: 1. Make a copy of the oplsaa.ff force field into your working directory 2. Modify its contents as needed to introduce any new atom types and bonded parameters 3. Write the .n2t file within that directory and make use of that one rather than any included in the force fields in $GMXLIB -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Graphene topology file
Hi Sukriti, Copy the oplsaa.ff directory to your working directory. Then in ffnonbonded.itp file add the following lines.. opls_995 C 612.01100 0.000 A3.4e-01 3.61200e-01 opls_996 C 612.01100 0.000 A3.4e-01 3.61200e-01 opls_997 C 612.01100 0.000 A3.4e-01 3.61200e-01 Then in atomname2type.n2t file add the following lines. Copls_9950 12.011 2C 0.142 C 0.142 Copls_9960 12.011 3C 0.142 C 0.142 C 0.142 Copls_9970 12.011 1C 0.142 Then use g_x2top. This will work. Thanks Abhijit On Thu, Jul 3, 2014 at 3:11 PM, Dr. Vitaly Chaban vvcha...@gmail.com wrote: Graphene topology is like for tube, so C C C ... C ... C C C C C to the N2T file and you are done. Dr. Vitaly V. Chaban On Wed, Jul 2, 2014 at 5:29 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/2/14, 9:56 AM, #SUKRITI GUPTA# wrote: Dear all, I want to simulate graphite in water, for which i am trying to create a topology file for graphite. As its .rtp file cannot be written correctly, i tried to use g_x2top command following the steps given in following tutorial. http://chembytes.wikidot.com/grocnt But I think this tutorial is quite old and hence suitable for older version of gromacs as it still uses FF.dat file. Moreover if i am trying to make a new forcefield directory with name graphite_oplsaa containing the modified files like .n2t,.rtp and .itp, its giving me an error that Could not find force field 'graphite_oplsaa' in current directory, install tree or GMXDATA path. When I try to add this forcefield in original path ie. user/share/gromacs/top, it does not allow me to do that as i am not the administrator. Can anyone please let me know how to create the topology file. I require 3 graphene sheets with pbc. I have created the .pdb file using nanobuilder in vmd. The tutorial is indeed outdated but the logic is fairly sound. You don't have to modify anything in $GMXLIB (system-wide); you can just create an .n2t file in the working directory and it will override the one at the force field level. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- 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. -- Abhijit kayal Research Scholar Theoretical Chemistry IIT Kanpur -- 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] Graphene topology file
Dear Justin and Abhijit, Thanks a lot for your help. Now I am able to make the topology file but while doing grompp for energy minimisation its not taking the dihedral values on its own. Regards Sukriti Sukriti Gupta (Ms) | PhD Student | Energy Research Institute @ NTU (ERI@N) | Nanyang Technological University Interdisciplinary Graduate School | Office: N1.3-B4-14, 62 Nanyang Drive, Singapore(637459) Tel: (65) 81164191 GMT+8h | Email:sukriti...@e.ntu.edu.sg | Web:erian.ntu.edu.sg From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of abhijit Kayal abhijitchemi...@gmail.com Sent: Thursday, July 3, 2014 6:43 PM To: gmx-us...@gromacs.org; vvcha...@gmail.com Subject: Re: [gmx-users] Graphene topology file Hi Sukriti, Copy the oplsaa.ff directory to your working directory. Then in ffnonbonded.itp file add the following lines.. opls_995 C 612.01100 0.000 A3.4e-01 3.61200e-01 opls_996 C 612.01100 0.000 A3.4e-01 3.61200e-01 opls_997 C 612.01100 0.000 A3.4e-01 3.61200e-01 Then in atomname2type.n2t file add the following lines. Copls_9950 12.011 2C 0.142 C 0.142 Copls_9960 12.011 3C 0.142 C 0.142 C 0.142 Copls_9970 12.011 1C 0.142 Then use g_x2top. This will work. Thanks Abhijit On Thu, Jul 3, 2014 at 3:11 PM, Dr. Vitaly Chaban vvcha...@gmail.com wrote: Graphene topology is like for tube, so C C C ... C ... C C C C C to the N2T file and you are done. Dr. Vitaly V. Chaban On Wed, Jul 2, 2014 at 5:29 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/2/14, 9:56 AM, #SUKRITI GUPTA# wrote: Dear all, I want to simulate graphite in water, for which i am trying to create a topology file for graphite. As its .rtp file cannot be written correctly, i tried to use g_x2top command following the steps given in following tutorial. http://chembytes.wikidot.com/grocnt But I think this tutorial is quite old and hence suitable for older version of gromacs as it still uses FF.dat file. Moreover if i am trying to make a new forcefield directory with name graphite_oplsaa containing the modified files like .n2t,.rtp and .itp, its giving me an error that Could not find force field 'graphite_oplsaa' in current directory, install tree or GMXDATA path. When I try to add this forcefield in original path ie. user/share/gromacs/top, it does not allow me to do that as i am not the administrator. Can anyone please let me know how to create the topology file. I require 3 graphene sheets with pbc. I have created the .pdb file using nanobuilder in vmd. The tutorial is indeed outdated but the logic is fairly sound. You don't have to modify anything in $GMXLIB (system-wide); you can just create an .n2t file in the working directory and it will override the one at the force field level. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- 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. -- Abhijit kayal Research Scholar Theoretical Chemistry IIT Kanpur -- 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
[gmx-users] Graphene topology file
Dear all, I want to simulate graphite in water, for which i am trying to create a topology file for graphite. As its .rtp file cannot be written correctly, i tried to use g_x2top command following the steps given in following tutorial. http://chembytes.wikidot.com/grocnt But I think this tutorial is quite old and hence suitable for older version of gromacs as it still uses FF.dat file. Moreover if i am trying to make a new forcefield directory with name graphite_oplsaa containing the modified files like .n2t,.rtp and .itp, its giving me an error that Could not find force field 'graphite_oplsaa' in current directory, install tree or GMXDATA path. When I try to add this forcefield in original path ie. user/share/gromacs/top, it does not allow me to do that as i am not the administrator. Can anyone please let me know how to create the topology file. I require 3 graphene sheets with pbc. I have created the .pdb file using nanobuilder in vmd. Thanks and Regards Sukriti [https://encrypted-tbn2.gstatic.com/images?q=tbn:ANd9GcQuwIkOr74lrv1_LpOuPBiUQ7Ai2kV8dmaAKtXKB0KYMUKxiIHSJg] http://www.google.com/imgres?imgurl=http%3A%2F%2Fwww.spms.ntu.edu.sg%2Fmas%2Fconference%2Ficits2013%2FICITS-2013-files%2Fntu-logo.jpgimgrefurl=http%3A%2F%2Fwww.spms.ntu.edu.sg%2Fmas%2Fconference%2Ficits2013%2Fh=59w=150tbnid=dMsKki52xFWVeM%3Azoom=1docid=XqAK8OLvcu_FUMei=xVyyU5q9A87j8AWMzYG4Cwtbm=ischved=0CFgQMygxMDEiact=rcuact=3dur=1673page=3start=41ndsp=27 Sukriti Gupta (Ms) | PhD Student | Energy Research Institute @ NTU (ERI@N) | Nanyang Technological University http://maps.ntu.edu.sg/maps#q:research%20techno%20plaza%20%28rtp%29 Interdisciplinary Graduate School | Office: N1.3-B4-14, 62 Nanyang Drive, Singapore(637459) Tel: (65) 81164191 GMT+8h | Email:sukriti...@e.ntu.edu.sgmailto:xx...@e.ntu.edu.sg | Web:erian.ntu.edu.sg http://www.ntu.edu.sg/home/xuzc/People.html -- 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] Graphene topology file
On 7/2/14, 9:56 AM, #SUKRITI GUPTA# wrote: Dear all, I want to simulate graphite in water, for which i am trying to create a topology file for graphite. As its .rtp file cannot be written correctly, i tried to use g_x2top command following the steps given in following tutorial. http://chembytes.wikidot.com/grocnt But I think this tutorial is quite old and hence suitable for older version of gromacs as it still uses FF.dat file. Moreover if i am trying to make a new forcefield directory with name graphite_oplsaa containing the modified files like .n2t,.rtp and .itp, its giving me an error that Could not find force field 'graphite_oplsaa' in current directory, install tree or GMXDATA path. When I try to add this forcefield in original path ie. user/share/gromacs/top, it does not allow me to do that as i am not the administrator. Can anyone please let me know how to create the topology file. I require 3 graphene sheets with pbc. I have created the .pdb file using nanobuilder in vmd. The tutorial is indeed outdated but the logic is fairly sound. You don't have to modify anything in $GMXLIB (system-wide); you can just create an .n2t file in the working directory and it will override the one at the force field level. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Graphene topology file
Dear Justin, Thanks for the reply but I am writing the .n2t file still getting the error that Could not find force field 'graphite_oplsaa' in current directory, install tree or GMXDATA path. What should I do? Moreover i don't think that n2t file tells program to use graphite_oplsaa force field. Regards Sukriti Sukriti Gupta (Ms) | PhD Student | Energy Research Institute @ NTU (ERI@N) | Nanyang Technological University Interdisciplinary Graduate School | Office: N1.3-B4-14, 62 Nanyang Drive, Singapore(637459) Tel: (65) 81164191 GMT+8h | Email:sukriti...@e.ntu.edu.sg | Web:erian.ntu.edu.sg From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Justin Lemkul jalem...@vt.edu Sent: Wednesday, July 2, 2014 11:29 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Graphene topology file On 7/2/14, 9:56 AM, #SUKRITI GUPTA# wrote: Dear all, I want to simulate graphite in water, for which i am trying to create a topology file for graphite. As its .rtp file cannot be written correctly, i tried to use g_x2top command following the steps given in following tutorial. http://chembytes.wikidot.com/grocnt But I think this tutorial is quite old and hence suitable for older version of gromacs as it still uses FF.dat file. Moreover if i am trying to make a new forcefield directory with name graphite_oplsaa containing the modified files like .n2t,.rtp and .itp, its giving me an error that Could not find force field 'graphite_oplsaa' in current directory, install tree or GMXDATA path. When I try to add this forcefield in original path ie. user/share/gromacs/top, it does not allow me to do that as i am not the administrator. Can anyone please let me know how to create the topology file. I require 3 graphene sheets with pbc. I have created the .pdb file using nanobuilder in vmd. The tutorial is indeed outdated but the logic is fairly sound. You don't have to modify anything in $GMXLIB (system-wide); you can just create an .n2t file in the working directory and it will override the one at the force field level. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- 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.
