[gmx-users] how to install GROMOS 43a1p force field in gromacs 4.5.5 version
Dear all please guide me how to install a new force field <http://www.gromacs.org/contributed_by_users/task,doc_download/gid,39/> GROMOS 43a1p <http://www.gromacs.org/contributed_by_users/task,doc_download/gid,39/> thank you all in adavance -- *Rajan kumar choudhary* *Senior Research Fellow* *Department of Atomic Energy(Govt.Of India)* *ACTREC TATA Memorial Center * *Kharghar Navi-Mumbai* *Mumbai-410210* *India * -- 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] Displacements of the components of the proteinn residue wise for the first eigenvector
hello every one, Actually i want to calculate Displacements of the components of the proteinn residue wise for the first eigenvector in gromacs. is thre is any option already present in gromacs for such calculation. thanks in advance-- -- *Rajan kumar choudhary* *Senior Research Fellow* *Department of Atomic Energy(Govt.Of India)* *ACTREC TATA Memorial Center * *Kharghar Navi-Mumbai* *Mumbai-410210* *India* -- 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] NMA in gromacs
Dear all, I have just started learning gromacs and want to do normal mode analysis of my protein. I don't know how nma.mdp file can be fetched or modified any help in this context is appriciated. with regards R ajan kumar choudhary *Senior Research Fellow* *Department of Atomic Energy(Govt.Of India)* *ACTREC TATA Memorial Center * *Kharghar Navi-Mumbai* *Mumbai-410210* *India* -- 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] NMA with gromacs trajectory
Dear all, Is it possible to perform Normal mode analysis and GNM analysis with gromacs trajectory file in GROMACS or somewhere else. any help in this regard will be very appreciated. thank you all -- *Rajan kumar choudhary* *Senior Research Fellow* *Department of Atomic Energy(Govt.Of India)* *ACTREC TATA Memorial Center * *Kharghar Navi-Mumbai* *Mumbai-410210* *India* -- 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] .xtc to DCD conversion
Dear all, Is it possible to convert .XTC(gromacs trajectory output) in to .DCD format for cross-correlation analysis using VMD 1.9.1 . any help in this regards will be appriciated. regards -- *Rajan kumar choudhary* *Senior Research Fellow* *Department of Atomic Energy(Govt.Of India)* *ACTREC TATA Memorial Center * *Kharghar Navi-Mumbai* *Mumbai-410210* *India* -- 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] how to make average hbond plot in gromacs using xmgrace
Dear all, i am trying to reduce the variation in the h-bond plot in xmgrace. can we reduce it and how? any help will be very appreciated with best regards -- *Rajan kumar choudhary* *Senior Research Fellow* *Department of Atomic Energy(Govt.Of India)* *ACTREC TATA Memorial Center * *Kharghar Navi-Mumbai* *Mumbai-410210* *India* -- 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] LINCS waring during MD.
Hi all, I am trying to study wetting of water on Graphene oxide(GO). Energy minimization for my gives me following result which, I think is ok. - Step= 5137, Dmax= 1.1e-06 nm, Epot= -9.40777e+03 Fmax= 4.76973e+01, atom= 2237 Step= 5138, Dmax= 1.3e-06 nm, Epot= -9.40776e+03 Fmax= 4.63983e+01, atom= 2237 Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax 20 Double precision normally gives you higher accuracy. writing lowest energy coordinates. Steepest Descents converged to machine precision in 5139 steps, but did not reach the requested Fmax 20. Potential Energy = -9.4077695e+03 Maximum force = 4.7697334e+01 on atom 2237 Norm of force = 3.9314783e+00 --- Since, I don't have solvent in my system, just a water droplet, I proceeded directly to mdrun, which gives me the usual LINCS warning after a few steps. Step 649931, time 649.931 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000283, max 0.002029 (between atoms 3008 and 3010) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 3008 3009 31.10.0949 0.0951 0.0950 --- Program mdrun, VERSION 4.5.5 Source code file: constr.c, line: 189 Fatal error: Too many LINCS warnings (1000) --- Same system with same mdp(http://goo.gl/Fx66sO) setting, I ran for 500 ps does not give any error. Please help me identify the problem. -- Rajan Kumar Indian Institute of Technology, Guwahati -- 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] Format of bond type directives
Hi all, I am using g_x2top to create topology for my system. After creating topology file, I see [ bonds ] ; aiaj functc0c1c2c3 1 3 1 1.42e-01 4.00e+05 1.42e-01 4.00e+05 1 4 1 1.42e-01 4.00e+05 1.42e-01 4.00e+05 1 5 1 1.39e-01 4.00e+05 1.39e-01 4.00e+05 2 3 1 1.42e-01 4.00e+05 1.42e-01 4.00e+05 2 9 1 1.42e-01 4.00e+05 1.42e-01 4.00e+05 -- Please help me understand this format, as the manual explain these directive written as something like this: [ bonds ] ; aiajfunct b0kb 131 0.14310376560 121 0.14310376560 241 0.15230376560 -- Rajan Kumar Indian Institute of Technology, Guwahati -- 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] Placing system at the centre of the box.
Hi Tsjerk, Please see the box here https://www.dropbox.com/s/cu70fw2dmwaxl1x/Editconf.png?dl=0. On Sat, Mar 14, 2015 at 1:38 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Rajan, Do you see the box? From your output it is easily seen that the new center equals 0.5*boxvectors. Cheers, Tsjerk On Mar 14, 2015 5:47 AM, Rajan Kumar kumarrajan...@gmail.com wrote: Hi all, I am trying to study wetting of water on Graphene oxide(GO). My structure has functional group in form of epoxide group on one side of the Graphene sheet. Also I have added water molecules in form of spherical droplet on the same side of the sheet. I used the following commands to generate .gro. editconf -f GO.pdb -o conf.gro -box 3 3 3 -angles 90 90 90 -c - Read 260 atoms No velocities found system size : 1.845 1.562 1.523 (nm) center : 0.985 0.828 0.380 (nm) box vectors : 0.000 0.000 0.000 (nm) box angles : 0.00 0.00 0.00 (degrees) box volume : 0.00 (nm^3) shift : 0.515 0.672 1.120 (nm) new center : 1.500 1.500 1.500 (nm) new box vectors : 3.000 3.000 3.000 (nm) new box angles : 90.00 90.00 90.00 (degrees) new box volume : 27.00 (nm^3) My question is, what is this* center* and how is it calculated by editconf? When I see conf.gro in VMD, I don't actually see my system at the geometric center of the box. -- Rajan Kumar Indian Institute of Technology, Guwahati -- 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. -- Rajan Kumar Indian Institute of Technology, Guwahati -- 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] Placing system at the centre of the box.
Hi all, I am trying to study wetting of water on Graphene oxide(GO). My structure has functional group in form of epoxide group on one side of the Graphene sheet. Also I have added water molecules in form of spherical droplet on the same side of the sheet. I used the following commands to generate .gro. editconf -f GO.pdb -o conf.gro -box 3 3 3 -angles 90 90 90 -c - Read 260 atoms No velocities found system size : 1.845 1.562 1.523 (nm) center : 0.985 0.828 0.380 (nm) box vectors : 0.000 0.000 0.000 (nm) box angles : 0.00 0.00 0.00 (degrees) box volume : 0.00 (nm^3) shift : 0.515 0.672 1.120 (nm) new center : 1.500 1.500 1.500 (nm) new box vectors : 3.000 3.000 3.000 (nm) new box angles : 90.00 90.00 90.00 (degrees) new box volume : 27.00 (nm^3) My question is, what is this* center* and how is it calculated by editconf? When I see conf.gro in VMD, I don't actually see my system at the geometric center of the box. -- Rajan Kumar Indian Institute of Technology, Guwahati -- 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] GNM from .xtc file
Dear all, I am having 50ns simulation data and i want to perform GNM. Any help will be very helpful. Regards and thank you -- *Rajan kumar choudhary* *Senior Research Fellow* *Department of Atomic Energy(Govt.Of India)* *ACTREC TATA Memorial Center * *Kharghar Navi-Mumbai* *Mumbai-410210* *India* -- 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] hello every one
-- *Rajan kumar choudhary* *Senior Research Fellow* *Department of Atomic Energy(Govt.Of India)* *ACTREC TATA Memorial Center * *Kharghar Navi-Mumbai* *Mumbai-410210* *India* -- 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] HOW TO CONVERT .XTC FILE TO DCD FORMAT
Dear all , i want to convert .xtc file to dcd format. Is it possible in gromacs command line. if not how i could be able to convert .xtc file in to dcd file format. thank you all -- *Rajan kumar choudhary* *Senior Research Fellow* *Department of Atomic Energy(Govt.Of India)* *ACTREC TATA Memorial Center * *Kharghar Navi-Mumbai* *Mumbai-410210* *India* -- 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] HOW TO CONVERT .XTC FILE TO DCD FORMAT
THANK YOU ALL FOR YOUR SUGGESTIONS. REGARDS On Fri, Feb 20, 2015 at 7:28 PM, Justin Lemkul jalem...@vt.edu wrote: On 2/20/15 8:40 AM, rajan kumar wrote: Dear all , i want to convert .xtc file to dcd format. Is it possible in gromacs command line. if not how i could be able to convert .xtc file in to dcd file format. http://bit.ly/1JtMPk4 :) -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- *Rajan kumar choudhary* *Senior Research Fellow* *Department of Atomic Energy(Govt.Of India)* *ACTREC TATA Memorial Center * *Kharghar Navi-Mumbai* *Mumbai-410210* *India* -- 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 Topology file
Hi all, I am trying to study wetting of water on Graphene oxide(GO). My structure has functional group in form of Hydroxyl and epoxide group on one side of the Graphene sheet. Also I have added water molecules in form of spherical droplet on the same side of the sheet. I used the following commands to generate .gro and topology file. editconf -f GO.pdb -o conf.gro -box 3 3 3 -angles 90 90 90 g_x2top -f conf.gro -o topol.top -ff oplsaa_GO My topology file is generated, but it show that there is a overall charge in the system, which I didn't expect. All files can be accessed at https://www.dropbox.com/sh/rtxg36y4pv2zwto/AADoQ_Y239XuSXK7-_4PNGJ_a?dl=0 So,I opened my topology file and I see -- 328 opls_116 2SOL OW328 -0.82 15.999 ; qtot -0.82 329 opls_168 2SOLHW1328 0 1.008 ; qtot -0.82 330 opls_168 2SOLHW2328 0 1.008 ; qtot -0.82 -- I have two different type of hydrogen in my .atp file, one for 'OH' on Graphene and other for water molecule. I have also specified their separate connectivity and chrages in .n2t file. However, from my topology file, I see that only one type of hydrogen atom (i.e. one corresponding to 'OH' of graphene, which doesn't have any charge) is present in topology file, due to which there is overall charge on the system. Any idea why this might be happening? -- Rajan Kumar Indian Institute of Technology, Guwahati -- 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 topology using g_x2top
Hi all, I am trying to study wetting of water on Graphene oxide(GO). My structure has functional group in form of Hydroxyl and epoxide group on only one side of the Graphene sheet. Also I have added water molecules in form of spherical droplet on the same side of the sheet. Since my simulation will be periodic in the plane of the GO sheet, I have not capped edges with hydrogen. I have created atomtypes.atp and atomname2type.n2t based on connectivity of individuals atoms and added them to force field file(oplsaa_GO.ff) in the working directory(Thanks Justin Lemkul for Suggestion). Also, I have copied original opls-aa ffnonded and ffnonbonded topology files to my working directory. Have a look at my files here https://www.dropbox.com/sh/rtxg36y4pv2zwto/AADoQ_Y239XuSXK7-_4PNGJ_a?dl=0 After creating .gro using editconf, I generate topology using g_x2top which gives me following error. g_x2top -f conf.gro -o topol.top -ff oplsaa_GO Opening force field file ./oplsaa_GO.ff/atomname2type.n2t There are 11 name to type translations in file ./oplsaa_GO.ff Generating bonds from distances... atom 420 Can not find forcefield for atom OS-9 with 5 bonds Can not find forcefield for atom OH-10 with 8 bonds Can not find forcefield for atom HO-11 with 8 bonds Can not find forcefield for atom OS-20 with 11 bonds Can not find forcefield for atom OH-21 with 16 bonds Can not find forcefield for atom HO-22 with 10 bonds Can not find forcefield for atom OS-31 with 12 bonds Can not find forcefield for atom OH-32 with 10 bonds Can not find forcefield for atom HO-33 with 13 bonds Can not find forcefield for atom OS-42 with 6 bonds Can not find forcefield for atom OH-43 with 13 bonds Can not find forcefield for atom OS-325 with 4 bonds Can not find forcefield for atom OH-326 with 7 bonds Can not find forcefield for atom HO-327 with 8 bonds - -- Can not find forcefield for atom HW2-414 with 13 bonds Can not find forcefield for atom OW-415 with 4 bonds Can not find forcefield for atom HW1-416 with 3 bonds Can not find forcefield for atom HW2-417 with 2 bonds Can not find forcefield for atom OW-418 with 20 bonds Can not find forcefield for atom HW1-419 with 9 bonds Can not find forcefield for atom HW2-420 with 6 bonds --- Program g_x2top, VERSION 4.5.5 Source code file: g_x2top.c, line: 206 Fatal error: Could only find a forcefield type for 238 out of 420 atoms Please help me out here. -- Rajan Kumar Indian Institute of Technology, Guwahati -- 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] Element naming format in .pdb file
Dear all, I am trying to study wetting of Graphene oxide. I have prepared a structure file using material studio, which I will simulate in GROMACS. My structure contain some epoxy and hydroxyl functional group in Graphene sheet. However, the structure file generated does not differentiate between carbon atoms with and without functional group in the Name column of .pdb file. Also there is no differentiation in naming format of oxygen atom in epoxy and hydroxyl group. Since, these atoms will have different atom type in atomtype.atp file of force filed.(I will be using OPLS-AA for simulation). Do I have to make edits in .pdb file for different atomtypes as well. Thanks Rajan Kumar Department of Chemical Engineering Indian Institute of Technology, Guwahati -- 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.
