[gmx-users] Question about water insertion
I have one water molecule in my gro file as below: TIP4P 4 1SOL OW1 0.054 0.005 0.022 1SOLHW12 0.009 0.072 0.073 1SOLHW23 0.142 0.041 0.008 1SOL MW4 0.060 0.018 0.026 0.00 0.000 0.000 Then use the command bellow to generate 13853 water molecules in the box. "insert-molecules -ci water.gro -box 10.1103 10.34753 3.958 -nmol 13853 -o insert.gro" But, the water did not settle during energy minimization. When I reduced the numebr of water to 5000, it works, but it does not have the correct density. I need 13853 number of molecules. It seems that gmx insert generates water without considering the correct distance between them. Do you have any idea to solve this problem? Thank you in advance! Golnaz -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] gmx solvate problem
Hi All, I’m simulating a box of tip4p ice. when I use the gmx solvate to fill the top and below part of the ice surface with solvent (the solvent is tip4p water), some of water molecules go to inside of the ice layers. I did not receive any errors, but the coordinate files became messy after salvation. I don't know how can I insert water molecules on the top and bellow of the surface correctly. Thank you in advance for any help, Golnaz -- 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] selecting atoms in index file
On Thu, Sep 7, 2017 at 12:35 PM, < gromacs.org_gmx-users-requ...@maillist.sys.kth.se> wrote: > Send gromacs.org_gmx-users mailing list submissions to > gromacs.org_gmx-users@maillist.sys.kth.se > > To subscribe or unsubscribe via the World Wide Web, visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > or, via email, send a message with subject or body 'help' to > gromacs.org_gmx-users-requ...@maillist.sys.kth.se > > You can reach the person managing the list at > gromacs.org_gmx-users-ow...@maillist.sys.kth.se > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of gromacs.org_gmx-users digest..." > > > Today's Topics: > >1. Re: selecting atoms in index file (Hermann, Johannes) >2. Re: DPOSRES not working (Hermann, Johannes) >3. Re: DPOSRES not working (Sergio Manzetti) >4. Re: DPOSRES not working (Hermann, Johannes) >5. Re: DPOSRES not working (Sergio Manzetti) > > > -- > > Message: 1 > Date: Thu, 7 Sep 2017 11:16:08 +0200 > From: "Hermann, Johannes" <j.herm...@lrz.tu-muenchen.de> > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] selecting atoms in index file > Message-ID: <c1fd2b6b-91f9-5ec7-d39d-4b666599a...@lrz.tum.de> > Content-Type: text/plain; charset=utf-8; format=flowed > > Dear Golnaz, > > do you know the number (index) of the respective atoms? E.g. open the > .gro file in vmd and look for the atoms? > > If there are not too many atoms, you can manually edit your index file. > E.g. create a default index file (gmx make_ndx) and add the subset of > indexes with a new selection definition: > > --- > > [ MySelection] > > 23 57 75 > > --- > > All the best > > Johannes > > Hi Johanne, > > Thank you for your reply. just one more question: when I edit atoms in my > index file, should I delete these atoms from surfaces groups. let me > explain better. Now I have 2 groups in my index file Sol and > Kaoli(surface). I should select some atoms from the Kaoli. So first I > define the atoms that I want to select in a seperate group, then I should > erase these atoms from kaoli parts. Am I right? because I want to freeze > the surface without these atoms. > > On 07.09.2017 11:02, G R wrote: > > Dear All, > > > > I want to create an index file and select some especial atoms in a > surface. > > My problem is that I have only one residue for the whole surface. How > can I > > select the atoms on the surface as a different groups in my index file? > > > > Thank you in advance, > > Golnaz > > -- > __ > *Technische Universit?t M?nchen* > *Johannes Hermann, M.Sc.* > Lehrstuhl f?r Bioverfahrenstechnik > Boltzmannstr. 15 > D-85748 Garching > Tel: +49 8928915730 > Fax: +49 8928915714 > > Email: j.herm...@lrz.tum.de > http://www.biovt.mw.tum.de/ > > > > -- > > Message: 2 > Date: Thu, 7 Sep 2017 11:18:29 +0200 > From: "Hermann, Johannes" <j.herm...@lrz.tu-muenchen.de> > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] DPOSRES not working > Message-ID: <8c01673e-77d8-fa16-c5ad-ec0269a47...@lrz.tum.de> > Content-Type: text/plain; charset=utf-8; format=flowed > > Dear Sergio, > > how did you define the position restrain in your topology? Check your > topology and position restrain file. > > All the best > > Johannes > > > On 07.09.2017 11:07, Sergio Manzetti wrote: > > Hello, I am running 5 simulations with the given mdp: > > > > title = DNA in water stabilization > > cpp = /lib/cpp > > include = -I../top > > define = -DPOSRES > > integrator = md > > dt = 0.002 > > nsteps = 1000 > > nstxout = 5000 > > nstvout = 5000 > > nstlog = 5000 > > nstenergy = 300 > > nstxout-compressed = 300 > > compressed-x-grps = PRB SOL NA CL DNA > > energygrps = PRB SOL NA CL DNA > > nstlist = 10 > > ns-type = grid > > rlist = 0.8 > > coulombtype = PME > > rcoulomb = 0.8 > > rvdw = 0.8 > > tcoupl = V-Rescale > > tc-grps = System > > tau-t = 0.1 > > ref-t = 310 > > Pcoupl = No > > tau-p = 1.0 > > compressibility = 4.5e-5 > > ref-p = 1.0 > > gen-vel = yes > > gen-temp = 310 > > gen-seed = 17527 > > constraints = all-bonds > > > > > > and still, the DNA splits into two > > > > Any ideas what could be wrong? > > > > Thanks > &
[gmx-users] selecting atoms in index file
Dear All, I want to create an index file and select some especial atoms in a surface. My problem is that I have only one residue for the whole surface. How can I select the atoms on the surface as a different groups in my index file? Thank you in advance, Golnaz -- 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] clayff forcefield
Dear usres, I try to write clayff forcefield, and I want to simulate Kaolinite. I have some questions about it. 1) should I write clayff forcefield separately or modify one of the forcefields in share/top? 2) The directory for clayff forcefield should be included ffbonded.itp, ffnonbonded.itp, atomname2type.n2t, forcefield.itp, forcefield.doc,atomtype.atp? if it is needed any other file please let me know? 3) In .n2t file, the first column should be written corresponding .gro file? 4) For Kaolinite I only have two type of Oxygen, ob (bridging oxygen) and oh (oxygen in hydroxyl group). Am I right? Any help will be appreciated, Golnaz -- 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] Could not find clayff forcefield
Dear users, I try to implement Clayff forcefield for Kaolinite. I created my force field (I'm not sure about it), but gromacs couldn't find my force field in the directory. Here is my forcefield. ffnonbonded [ atomtypes ] ; name mass chargeptype sigma eps HW 1 1.00800 0.4100A0.0e-01 0.0e-01 ;clayFF_waterhydrogen HO 1 1.00800 0.4250A0.0e-01 0.0e-01 ;clayFF_hydroxylhydrogen OW 8 15.99800-0.8200A3.16557e-01 6.50209e-01 ;ClayFF_wateroxygen OH 8 15.99800-0.9500A3.16557e-01 6.50209e-01 ;ClayFF_hydroxyloxygen OB 8 15.99800-1.0500A3.16557e-01 6.50209e-01 ;ClayFF_bridgingoxygen OBOS 8 15.99800-1.1808A3.16557e-01 6.50209e-01 ;ClayFF_bridgingoxygenoctasub OBTS 8 15.99800-1.1688A3.16557e-01 6.50209e-01 ;ClayFF_bridgingoxygentetrsub OHS 8 15.99800-1.0808A3.16557e-01 6.50209e-01 ;ClayFF_hydroxyloxygensub SI 14 28.08600 2.1000A3.30208e-01 8.0e-06 ;ClayFF_tetrahedralsilicon AO 13 26.98200 1.5750A4.27128e-01 6.0e-06 ;ClayFF_octahedalaluminium AT 13 26.98200 1.5750A3.30206e-01 8.0e-06 ;ClayFF_tetrasubaluminium ffbonded [ bondtypes ] ; ij func b0 kb OW HW 10.1000 554134.9 OH HO 10.1000 554134.9 OHSHO 10.1000 554134.9 [ angletypes ] ; ijk func th0 cth HW OWHW1109.47191.564 AL OHHO1109.47125.52 atomtype.n2t HHW0.4100 1.008 1O 0.100 ;water hydrogen OOW -0.820015.998 2H 0.100H 0.100 ;water oxygen OH2 OH -0.950015.998 1H 0.100 ;hydroxyl oxygen O2 obts -1.1688 15.998 0;bridging oxygen with tetrahedral substitution O1 obss -1.2996 15.998 0 ;bridging oxygen with double substitution OH1 ohs -1.0808 15.998 1 H 0.100 ;hydroxyl hydrogen with substitution Si st2.100028.086 0 ;tetrahedral silicon Al ao1.575026.982 0 ;octahedral aluminium Mg mgo1.360024.305 0 ; octahedral magnisium Na Na1.22.999 0 ;sodium ion forcefield.doc clayff.ff force field forcefield.itp #define _ff_clayff [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ 1 3 yes 0.5 0.5 #include "ffnonbonded.itp" #include "ffbonded.itp" pdb Al0.6494.3333.377 Al3.248.8053.377 Al3.2032.8513.362 Al0.6397.3243.362 Si4.9623.0160.65 Si2.3987.4880.65 Si2.4421.470.653 Si-0.1225.9420.653 O1-0.3343.0982.268 O12.2587.572.268 O10.0415.8392.271 O12.6051.3672.271 O30.0144.4720 O3-1.8854.2597.154 O35.1694.4720 O33.274.2597.154 O32.57800 O30.678-0.2147.154 O32.6058.9450 O30.7068.7317.154 O31.0342.0560.177 O33.6266.5290.177 O31.0526.8480.023 O33.6162.3760.023 OH1-0.3228.6062.304 OH12.2424.1332.304 OH23.831.364.329 OH21.2665.8324.329 OH2-0.9624.1364.35 OH21.6298.6084.35 OH2-0.9617.5354.36 OH21.6023.0634.36 O22.63310.3122.271 OH23.85810.3054.329 OH24.8348.6062.304 OH24.1947.5354.36 O34.8213.0982.268 OH34.1934.1364.35 O36.192.0560.177 O3-1.5296.5290.177 It's to long, Sorry about it, but I really need to find out where is my problem. I put n2t file in directory not in my forcefield subdirectory. Do I need to create any other file for clayff forcefield? Thank you in advece, Golnaz -- 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] Clayff forcefield
I try to implement CLYFF in gromacs. I created ffbonded.itp, ffnonbonded.itp, atomtype.atp, forcefield.doc, forcefield.itp and molecule.rtp. I want to simulate Kaolinite, and I try to use pdb2gmx to create a topology. My first question is that should I create any other files? second, In molecule.rtp, I just write the atom type, atom name and charges. should I add bonds for each atom? Also, in rtp file, I don't know what should I write as a residue? Thank you in advance, Golnaz -- 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] TIP4P/ice pdb file
Dear Chris, Yes, tip4p.gro worked well. Thank you On Wed, Jul 5, 2017 at 10:55 PM, < gromacs.org_gmx-users-requ...@maillist.sys.kth.se> wrote: > Send gromacs.org_gmx-users mailing list submissions to > gromacs.org_gmx-users@maillist.sys.kth.se > > To subscribe or unsubscribe via the World Wide Web, visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > or, via email, send a message with subject or body 'help' to > gromacs.org_gmx-users-requ...@maillist.sys.kth.se > > You can reach the person managing the list at > gromacs.org_gmx-users-ow...@maillist.sys.kth.se > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of gromacs.org_gmx-users digest..." > > > Today's Topics: > >1. TIP4P/ice pdb file (G R) >2. Re: simulation at different temperature (Alex) >3. Re: simulation at different temperature (Alex) >4. Re: TIP4P/ice pdb file (Christopher Neale) >5. Re: TIP4P/ice pdb file (Christopher Neale) > > > ------ > > Message: 1 > Date: Wed, 5 Jul 2017 21:57:26 +0300 > From: G R <golnaz.c...@gmail.com> > To: gromacs.org_gmx-users@maillist.sys.kth.se > Subject: [gmx-users] TIP4P/ice pdb file > Message-ID: >
[gmx-users] TIP4P/ice pdb file
Dear All, I would like to simulate water using TIP4P/ice potential. My question is that how can I generate .gro file for this simulation? I will use TIP4P/ice topology that is available in SklogWiki, but I cannot understand how can I generate .gro file for this topology. Can I easily use TIP4P.gro that is available in share/top? If yes, how can I modify TIP4P.gro file to use with TIP4P/ice potential? Best regards, Golnaz -- 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] Simulation of pure water
Dear all, I want to calculate the relaxation of pure water cell at room temperature and at freezing point, monitoring its equilibration in volume and in potential energy. I have 3 question: 1) Can I use packmol for my initial configuration? if there is any other option,please tell me. 2) Can I use easily pdb2gmx to generate the topology file? 3) Which Forcefield is better for this calculation? I'v already read some tutorial, but if you have any suggestion it woulb be appreciated. Thank you in advanc -- 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] Simulation of pure water
Dear all, I want to calculate the relaxation of pure water cell at room temperature and at freezing point, monitoring its equilibration in volume and in potential energy. I have 3 question: 1) Can I use packmol for my initial configuration? if there is any other option,please tell me. 2) Can I use easily pdb2gmx to generate the topology file? 3) Which Forcefield is better for this calculation? I'v already read some tutorial, but if you have any suggestion it woulb be appreciated. Thank you in advance GR -- 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.
